package slidingwindow;

import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.Random;

public class RunThreads implements Runnable  {


	private final double stat;
	private final Integer sims;
	private ArrayList<String> windows = new ArrayList<String>();
	private ArrayList<String> predictions = new ArrayList<String>();

	public RunThreads(ArrayList<String> windows1, ArrayList<String> predictions1, double stat1, Integer sims1){
		this.windows = windows1;
		this.predictions = predictions1;
		this.stat = stat1;
		this.sims = sims1;
	}

	public void run() {
		for(String window: windows) {
			String[] windowParts = window.split("\t");
			Integer firstPart = Integer.parseInt(windowParts[0]);
			Integer secondPart = Integer.parseInt(windowParts[1]);
			Integer firstMean = FindMeanSites(firstPart, stat, predictions, sims);
			Integer secondMean = FindMeanSites(secondPart, stat, predictions, sims);
			Integer slope = (secondMean - firstMean);
			System.out.println(firstPart + "\t" + secondPart + "\t" + slope);
		}
	}

	public Integer FindMeanSites(Integer countReads, Double percentComplete, ArrayList<String> readArray, Integer sims) {
		Integer meanCount = 0;
		Integer simSlope = 0;
		Integer totalSlope = 0;
		for(Integer j = 0; j < sims; j++) {
			long seedValue = System.nanoTime();
			Collections.shuffle(readArray, new Random(seedValue));
			simSlope = GetSiteCount(countReads, percentComplete, readArray);
			totalSlope += simSlope;
		}
		meanCount = totalSlope/sims;
		return meanCount;
	}

	public Integer GetSiteCount(Integer count, Double percent, ArrayList<String> reads) {
		Integer totalCount = 0;
		HashMap<String, String> found = new HashMap<String,String>();
		found.clear();
		Integer k = 0;
		for(Integer j = 0; j < count; j++) {
			long seed = System.nanoTime();
			Random generator = new Random(seed);
			double r = generator.nextDouble();
			if(r <= percent){
				String site = reads.get(k);
				k++;
				if(found.containsKey(site)) {
				} else {
					totalCount++;
					found.put(site, "FOUND");
				}
			}
		}
		return totalCount;
	}


}