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/**********************************************************************
* file: codonMSA.hh
* licence: Artistic Licence, see file LICENCE.TXT or
* http://www.opensource.org/licenses/artistic-license.php
* descr.: datastructure for the codon alignment
* author: Lizzy Gerischer
*
* date | author | changes
* --------|--------------------|------------------------------------------
* 14.07.16| Lizzy Gerischer | creation of the file
**********************************************************************/
#ifndef _CODONMSA
#define _CODONMSA
#include <fstream>
#include "properties.hh"
#include "phylotree.hh"
#include "contTimeMC.hh"
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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