protected void constructRateMap(){
  rateMap=Codons.constructRateMap(rateCount,stateCount,codonDataType,geneticCode);
}

protected void constructRateMap ( ) { rateMap = Codons . constructRateMap ( rateCount , stateCount , codonDataType , geneticCode ) ; }
construct a map of the rate classes in the rate matrix using the current genetic code . classes : 0 : codon changes in more than one codon position ( or stop codons ) 1 : synonymous transition 2 : synonymous transversion 3 : non - synonymous transition 4 : non - synonymous transversion
