src/CombingExperimentSimulation.java
/**
     * Prints RMS deviation of Observed and Predicted Fork numbers for Kaykov and Nurse dataset
     * @param predictedFxFilter predicate giving filter for fraction replicated
     * @param pset the parameter set
     */
Prints RMS deviation of Observed and Predicted Fork numbers for Kaykov and Nurse dataset
@param predictedFxFilter predicate giving filter for fraction replicated
@param pset the parameter set
Prints RMS deviation of Observed and Predicted Fork numbers for Kaykov and Nurse dataset @param predictedFxFilter predicate giving filter for fraction replicated @param pset the parameter set
public static void printRmsDeviationObservedAndPredictedForkNumbers (Predicate<PopulationAveragesCombingSimulation> predictedFxFilter, ParameterSet pset) {
        List<PopulationAveragesCombingSimulation> averages = population.getAverageStateVariablesForCombedMolecules();
        List<PopulationAveragesCombingSimulation> filteredAverages = averages.stream().filter(predictedFxFilter).collect(toList());
        double totalSqDeviation = 0.0;
        for (PopulationAveragesCombingSimulation ave : filteredAverages) {
            totalSqDeviation += (ave.getReferenceMoleculeForksPerMb()- ave.getForksPerMb()) * (ave.getReferenceMoleculeForksPerMb()- ave.getForksPerMb());
        }
        System.out.println("RMS deviation"+ "\t" + "RateIncrease" + "\t" + "MaxRate" );
        System.out.println(Math.sqrt(totalSqDeviation / filteredAverages.size()) + "\t" + pset.getTimeConstant() + "\t" + pset.getMaxFiringProbabilityPerMin());
    }
public static void printRmsDeviationObservedAndPredictedForkNumbers ( Predicate < PopulationAveragesCombingSimulation > predictedFxFilter , ParameterSet pset ) { List < PopulationAveragesCombingSimulation > averages = population . getAverageStateVariablesForCombedMolecules ( ) ; List < PopulationAveragesCombingSimulation > filteredAverages = averages . stream ( ) . filter ( predictedFxFilter ) . collect ( toList ( ) ) ; double totalSqDeviation = 0.0 ; for ( PopulationAveragesCombingSimulation ave : filteredAverages ) { totalSqDeviation += ( ave . getReferenceMoleculeForksPerMb ( ) - ave . getForksPerMb ( ) ) * ( ave . getReferenceMoleculeForksPerMb ( ) - ave . getForksPerMb ( ) ) ; } System . out . println ( "RMS deviation" + "\t" + "RateIncrease" + "\t" + "MaxRate" ) ; System . out . println ( Math . sqrt ( totalSqDeviation / filteredAverages . size ( ) ) + "\t" + pset . getTimeConstant ( ) + "\t" + pset . getMaxFiringProbabilityPerMin ( ) ) ; }
Prints RMS deviation of Observed and Predicted Fork numbers for Kaykov and Nurse dataset
 @param predictedFxFilter predicate giving filter for fraction replicated
 @param pset the parameter set
Prints RMS deviation of Observed and Predicted Fork numbers for Kaykov and Nurse dataset @param predictedFxFilter predicate giving filter for fraction replicated @param pset the parameter set
//get averages list and filter it //calculate RMS deviation of predicted vs observed number forks