common.h

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

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