package slidingwindow;


import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;

public class SlidingWindowMultiThread {
	public static void main(String[] args) {
		// TODO Auto-generated method stub

		SlidingWindowMultiThread measureSlope = new SlidingWindowMultiThread();
		String predictedFile = args[0];
		String statsFile = args[1];
		String windowString = args[2];
		String stepString = args[3];
		String maxReads = args[4];
		String simulationNumber = args[5];
		String threadCount = args[6];
		Integer threads = Integer.parseInt(threadCount);
		Integer simulationCount = Integer.parseInt(simulationNumber);
		Integer maxInteger = Integer.parseInt(maxReads);
		Integer windowInteger = Integer.parseInt(windowString);
		Integer stepInteger = Integer.parseInt(stepString);
		ArrayList<String> predictionsUnformattedArray = new ArrayList<String>();
		ArrayList<String> statsUnformattedArray = new ArrayList<String>();
		try {
			predictionsUnformattedArray = measureSlope.loadFile(predictedFile);
			statsUnformattedArray = measureSlope.loadFile(statsFile);
		} catch(Exception e) {
			if(e instanceof IOException) {
				System.out.println("YOU GOOFED");
			}
		}

		ArrayList<String> predictionsArray = new ArrayList<String>();
		ArrayList<String> windowArray = new ArrayList<String>();
		double predPercent = 0;
		predictionsArray = measureSlope.FormatPredictions(predictionsUnformattedArray);
		predPercent = measureSlope.FormatStats(statsUnformattedArray);
		windowArray = measureSlope.MakeWindows(windowInteger, stepInteger, maxInteger);
		measureSlope.MakeThreads(threads, windowArray, predictionsArray, predPercent, simulationCount); // This is the part of the code where I try to multithread. See right below.
	}

	public void MakeThreads(Integer threads, ArrayList<String> windows, ArrayList<String> predictions, double stat, Integer simulations) {             // This is the subroutine that tries to multithread. Every other subroutine works
		ArrayList<String> windowSegment = new ArrayList<String>();
		Integer startValue = 0;
		Integer endValue = 0;
		Integer windowsSize = windows.size();
		Integer increment = windowsSize/threads;
		ExecutorService executor = Executors.newFixedThreadPool(threads);
		for(Integer j = 0; j < threads; j++) {
			endValue = startValue + increment;
			windowSegment.clear();
				for(Integer k = startValue; k < endValue; k++) {
					windowSegment.add(windows.get(k));
				}
			Runnable worker = new RunThreads(windowSegment, predictions, stat, simulations);
			executor.execute(worker);
		}
		executor.shutdown();
	}

	public double FormatStats(ArrayList<String> unformattedStats) {
		double predictedFraction = 0;
		String statLine = unformattedStats.get(0);
		String[] statLineParts = statLine.split("= ");
		String value = statLineParts[1];
		predictedFraction = Double.parseDouble(value);
		return predictedFraction;
	}

	public ArrayList<String> FormatPredictions(ArrayList<String> unformattedPredictions) {
		ArrayList<String> formattedPredictions = new ArrayList<String>();
		Integer lineNumber = 0;
		for(String predictionLine:unformattedPredictions) {
			lineNumber++;
			if(lineNumber > 1){
				String[] predictionLineParts = predictionLine.split("\t");
				String chrom = predictionLineParts[1];
				String start = predictionLineParts[2];
				String end = predictionLineParts[3];
				String countString = predictionLineParts[8];
				String siteLine = chrom + "\t" + start + "\t" + end;
				Integer count = Integer.parseInt(countString);
				if(count > 0){
					for(Integer j = 0; j < count; j++) {
						formattedPredictions.add(siteLine);
					}
				}
			}
		}
		return formattedPredictions;
	}

	public ArrayList<String> MakeWindows(Integer window, Integer step, Integer max) {
		ArrayList<String> windows = new ArrayList<String>();
		Integer start = 0;
		Integer end = window;
		String startString = Integer.toString(start);
		String endString = Integer.toString(end);
		String windowString = startString + "\t" + endString;
		windows.add(windowString);
		while(end <= max) {
			start += step;
			end += step;
			startString = Integer.toString(start);
			endString = Integer.toString(end);
			windowString = startString + "\t" + endString;
			windows.add(windowString);
		}
		return windows;
	}

	public ArrayList<String> loadFile(String fileName) throws IOException { // this subroutine loads the files

		FileReader fileReader = new FileReader(fileName);
		BufferedReader bufferedReader = new BufferedReader(fileReader);
		String line = null;
		ArrayList<String> fileLines = new ArrayList<String>();
		try {
			while ((line = bufferedReader.readLine()) != null) {
				fileLines.add(line);
			}
		}	finally {
			bufferedReader.close();
		}
		return fileLines;
	}


}