00001 00002 00006 //(c) 2006 Suzanne Matthews 00007 /* 00008 This file is part of the RaqApproach software package. 00009 00010 RaqApproach is free software; you can redistribute it and/or modify 00011 it under the terms of the GNU General Public License as published by 00012 the Free Software Foundation; either version 2 of the License, or 00013 (at your option) any later version. 00014 00015 RaqApproach is distributed in the hope that it will be useful, 00016 but WITHOUT ANY WARRANTY; without even the implied warranty of 00017 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 00018 GNU General Public License for more details. 00019 00020 You should have received a copy of the GNU General Public License 00021 along with RaqApproach; if not, write to the Free Software 00022 Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA 00023 */ 00024 #ifndef COMMON_H_ 00025 #define COMMON_H_ 00026 00027 #include <iostream> 00028 #include <fstream> 00029 #include <string> 00030 #include <list> 00031 #include <vector> 00032 #include <map> 00033 #include <sstream> 00034 00035 using namespace std; 00036 //****************** GLOBAL CONSTANTS ******************************************** 00037 const int lambda = 2; 00038 const double initial_q = .1; 00039 const int decay = 2; 00040 int num_taxa; 00041 const int gap_penalty = -1; 00042 const char gap_char = '-'; 00043 const char unknown_char = '?'; 00044 const bool DISPLAY = false; 00045 vector<char> unknown_chars; 00046 //******************************************************************************** 00047 00048 #endif