BayesFactorTest.java

package templates;

import gui.InteractiveTableModel;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.Comparator;
import java.util.List;

import readers.LogFileReader;

import utils.Holder;
import utils.Utils;
import utils.Utils.PoissonPriorEnum;

/**
 * Pass by reference
 * 
 * */

public class BayesFactorTest {

	private Holder meanPoissonPrior;
	private Holder poissonPriorOffset;

	private InteractiveTableModel table;
	private PoissonPriorEnum meanPoissonPriorSwitcher;
	private PoissonPriorEnum poissonPriorOffsetSwitcher;
	private LogFileReader indicators;
	private ArrayList<String> combin;
	private ArrayList<Double> bayesFactors;
	private ArrayList<Double> posteriorProbabilities;
	
	public BayesFactorTest(InteractiveTableModel table, //
 			PoissonPriorEnum meanPoissonPriorSwitcher, //
			Holder meanPoissonPriorHolder, //
			PoissonPriorEnum poissonPriorOffsetSwitcher, //
			Holder poissonPriorOffsetHolder, //
			LogFileReader indicators, //
			ArrayList<String> combin, // 
			ArrayList<Double> bayesFactors, //
			ArrayList<Double> posteriorProbabilities //
			) {

		this.table = table;
		this.meanPoissonPriorSwitcher = meanPoissonPriorSwitcher;
		this.meanPoissonPrior = meanPoissonPriorHolder;
		this.poissonPriorOffsetSwitcher = poissonPriorOffsetSwitcher;
		this.poissonPriorOffset = poissonPriorOffsetHolder;
		this.indicators = indicators;
		this.combin = combin;
		this.bayesFactors = bayesFactors;
        this.posteriorProbabilities = posteriorProbabilities;
		
	}

	public void ComputeBFTest() {

		int n = table.getRowCount();

		switch (meanPoissonPriorSwitcher) {
		case DEFAULT:
			meanPoissonPrior.value = Math.log(2);
			break;
		case USER:
			break;
		}

		switch (poissonPriorOffsetSwitcher) {
		case DEFAULT:
			poissonPriorOffset.value = (double) (n - 1);
			break;
		case USER:
			break;
		}

		boolean symmetrical = false;
		if (indicators.ncol == n * (n - 1)) {
			symmetrical = false;
		} else if (indicators.ncol == (n * (n - 1)) / 2) {
			symmetrical = true;
		} else {
			throw new RuntimeException(
					"the number of rate indicators does not match the number of locations!");
		}

		String[] locations = table.getColumn(0);

		for (int row = 0; row < n - 1; row++) {

			String[] subset = Utils.subset(locations, row, n - row);

			for (int i = 1; i < subset.length; i++) {
				combin.add(locations[row] + ":" + subset[i]);
			}
		}

		if (symmetrical == false) {

			List<String> combinReverse = new ArrayList<String>();
			for (int i = 0; i < combin.size(); i++) {
				String state = combin.get(i).split(":")[1];
				String parentState = combin.get(i).split(":")[0];
				combinReverse.add(state + ":" + parentState);
			}

			combin.addAll(combinReverse);
		}

		double qk = Double.NaN;
		if (symmetrical) {
			qk = (meanPoissonPrior.value + poissonPriorOffset.value)
					/ ((n * (n - 1)) / 2);
		} else {
			qk = (meanPoissonPrior.value + poissonPriorOffset.value)
					/ ((n * (n - 1)) / 1);
		}

		double[] pk = Utils.colMeans(indicators.indicators);
		
		double denominator = qk / (1 - qk);

		for (int row = 0; row < pk.length; row++) {
			double bf = (pk[row] / (1 - pk[row])) / denominator;

			if (bf == Double.POSITIVE_INFINITY) {

				bf = ((pk[row] - (double) (1.0 / indicators.nrow)) / (1 - (pk[row] - (double) (1.0 / indicators.nrow))))
						/ denominator;

				System.out.println("Correcting for infinite bf: " + bf);
			}// END: infinite BF check

			bayesFactors.add(bf);
			posteriorProbabilities.add(pk[row]);
		}// END: row loop

	}// END: ComputeBFTest

	/**
	 * @return array with sort order indices to be used to print bayesFactors
	 *         and combin lists in descending order
	 * */
	public Integer[] getSortOrder() {
		
		Integer[] sortOrder = new Integer[bayesFactors.size()];
		for (int i = 0; i < sortOrder.length; i++) {
			sortOrder[i] = i;
		}

		Arrays.sort(sortOrder, new Comparator<Integer>() {
			public int compare(Integer a, Integer b) {
				return (bayesFactors.get(b) > bayesFactors.get(a)) ? 1 : -1;
			}
		});
		
		return sortOrder;
	}// END: getSortOrder
	
}// END: BayesFactorTest