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/*
* codonMSA.hh
*
* License: Artistic License, see file LICENSE.TXT or
* https://opensource.org/licenses/artistic-license-1.0
*/
#ifndef _CODONMSA
#define _CODONMSA
#include <fstream>
#include "properties.hh"
#include "phylotree.hh"
#include "contTimeMC.hh"
#include "codonevo.hh"
/**
* @brief datastructure for the codon alignment
*
* @author Lizzy Gerischer
*/
class CodonMSA{
public:
CodonMSA(string filename, double branchlength);
~CodonMSA(){
delete ctree;
}
void readAlignment(string filename);
void printOmegaStats();
vector<string> aliRows;
vector<string> speciesNames;
size_t aliLen;
int refSpeciesIdx;
CodonEvo codonevo;
PhyloTree* ctree;
};
#endif
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