src/DnaSynthesisCycle2.java
/**
     * Returns true if site is passively replicated
     * @param site current potential initiation site
     * @return true if passively replicated site
     */
Returns true if site is passively replicated
@param site current potential initiation site
@return true if passively replicated site
Returns true if site is passively replicated @param site current potential initiation site @return true if passively replicated site
private boolean IsPassivelyReplicated(PotentialInitiationSite2 site) {
        if (site.getPosition() < leftEnd.getRightActivePIS().getPosition()) {  
            if (site.getPosition() < leftEndFork) {return false;}
        }
        else if (site.getPosition() > rightEnd.getLeftActivePIS().getPosition()) { 
            if (site.getPosition() > rightEndFork) {return false;}
        }
        else if (site.getPosition() > forkOnLeft && site.getPosition() < forkOnRight) {  
            return false;
        }
        return true;
    }
private boolean IsPassivelyReplicated ( PotentialInitiationSite2 site ) { if ( site . getPosition ( ) < leftEnd . getRightActivePIS ( ) . getPosition ( ) ) { if ( site . getPosition ( ) < leftEndFork ) { return false ; } } else if ( site . getPosition ( ) > rightEnd . getLeftActivePIS ( ) . getPosition ( ) ) { if ( site . getPosition ( ) > rightEndFork ) { return false ; } } else if ( site . getPosition ( ) > forkOnLeft && site . getPosition ( ) < forkOnRight ) { return false ; } return true ; }
Returns true if site is passively replicated
 @param site current potential initiation site
 @return true if passively replicated site
Returns true if site is passively replicated @param site current potential initiation site @return true if passively replicated site
//if in left interval before the first active //return true; //if in right interval after the last active //else {return true;} //if in other interval