trna.h

#ifndef __TRNA_H
#define __TRNA_H

// need a way to record mutations and their impacts
// would also be good to record parent of each gene

class gene {
public:

    /// position of the tRNA
    double locus ;

    /// the name of the tRNA - just a number unique for that run
    int name ;
    
    /// sequence
    double sequence ;

    /// genotype (meaningless unless --mutation-pathways is used)
    string genotype ;

	// expression
	double expression ;

    // frequency over time ;
    // vector<int> frequency ;

    // generation when gene was first seen
    int birth ;  

    /// u rates per locus
    double somatic ;
    double germline ;

    // progenitor 
    int progenitor ;

    // mode of birth (helps for traceback)
    char birth_mode ;

    // indel rate
    // float indel ;

    // number of mutations accumulated by this tRNA
    int muts ;
    
    // sort function
    bool operator <(const gene &g1 ) {
        return g1.locus > locus ;
    }

} ;

#endif