src/ReplicatingMolecule2.java
/**
     * Prints the major variables in the given synthesis cycle - mainly for testing
     * @param cycle the instance of DNASynthesisCycle of this molecule
     */
Prints the major variables in the given synthesis cycle - mainly for testing
@param cycle the instance of DNASynthesisCycle of this molecule
Prints the major variables in the given synthesis cycle - mainly for testing @param cycle the instance of DNASynthesisCycle of this molecule
void printState(DnaSynthesisCycle2 cycle) {
        System.out.println();
        System.out.println("Number Nucleotides Replicated   " + cycle.getNumberNucleotidesReplicated());
        System.out.println("Number Intiations   " + cycle.getInitiations());
        System.out.println("Number closures   " + cycle.getClosures());
        System.out.println("NumberTerminations   " + cycle.getTerminations());
        System.out.println("Number Passives   " + cycle.getPassives());
        System.out.println("Number Actives   " + cycle.getActives());
        System.out.println("Number Potentials   " + cycle.getPotentials());
        System.out.println("Elapsed Time   " + elapsedTime);
        System.out.format("Fraction Replicated   %.3f%n" ,(double)cycle.getNumberNucleotidesReplicated()/seqLength);
        System.out.println();
        if (!cycle.getLeftEnd().getRightActivePIS().IsLeftForkActive()) { 
            System.out.format("%10d   ", (int) 1);
            }
        potentialInitSitesList.stream().forEach(p -> {
            if (p.IsActive()) {
                if (p.IsLeftForkActive())     {
                    System.out.format("%10d   ",p.getPositionLeftFork());
                }
                if (p.IsRightForkActive()) {
                    System.out.format("%10d   %n",p.getPositionRightFork());
                }
            }
        });
        if (!cycle.getRightEnd().getLeftActivePIS().IsRightForkActive()) {
            System.out.format("%10d   %n",seqLength);
        }
    }
void printState ( DnaSynthesisCycle2 cycle ) { System . out . println ( ) ; System . out . println ( "Number Nucleotides Replicated   " + cycle . getNumberNucleotidesReplicated ( ) ) ; System . out . println ( "Number Intiations   " + cycle . getInitiations ( ) ) ; System . out . println ( "Number closures   " + cycle . getClosures ( ) ) ; System . out . println ( "NumberTerminations   " + cycle . getTerminations ( ) ) ; System . out . println ( "Number Passives   " + cycle . getPassives ( ) ) ; System . out . println ( "Number Actives   " + cycle . getActives ( ) ) ; System . out . println ( "Number Potentials   " + cycle . getPotentials ( ) ) ; System . out . println ( "Elapsed Time   " + elapsedTime ) ; System . out . format ( "Fraction Replicated   %.3f%n" , ( double ) cycle . getNumberNucleotidesReplicated ( ) / seqLength ) ; System . out . println ( ) ; if ( ! cycle . getLeftEnd ( ) . getRightActivePIS ( ) . IsLeftForkActive ( ) ) { System . out . format ( "%10d   " , ( int ) 1 ) ; } potentialInitSitesList . stream ( ) . forEach ( p -> { if ( p . IsActive ( ) ) { if ( p . IsLeftForkActive ( ) ) { System . out . format ( "%10d   " , p . getPositionLeftFork ( ) ) ; } if ( p . IsRightForkActive ( ) ) { System . out . format ( "%10d   %n" , p . getPositionRightFork ( ) ) ; } } } ) ; if ( ! cycle . getRightEnd ( ) . getLeftActivePIS ( ) . IsRightForkActive ( ) ) { System . out . format ( "%10d   %n" , seqLength ) ; } }
Prints the major variables in the given synthesis cycle - mainly for testing
 @param cycle the instance of DNASynthesisCycle of this molecule
Prints the major variables in the given synthesis cycle - mainly for testing @param cycle the instance of DNASynthesisCycle of this molecule
//first active left fork is  not active 