package edu.unc.genomics.converters;

import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import org.apache.log4j.Logger;

import com.beust.jcommander.Parameter;

import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.ReadablePathValidator;
import edu.unc.utils.RomanNumeral;

public class RomanNumeralize extends CommandLineTool {

	private static final Logger log = Logger.getLogger(RomanNumeralize.class);

	@Parameter(names = {"-i", "--input"}, description = "Input file", required = true, validateWith = ReadablePathValidator.class)
	public Path inputFile;
	@Parameter(names = {"-o", "--output"}, description = "Output file", required = true)
	public Path outputFile;
	
	/**
	 * Pattern for finding "chr12" tokens (will find "chr1" through "chr99")
	 */
	Pattern p = Pattern.compile("/chr[\\d]{1,2}/i");
	
	@Override
	public void run() throws IOException {
		try (BufferedReader reader = Files.newBufferedReader(inputFile, Charset.defaultCharset());
				 BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) {
			log.debug("Copying input to output and replacing with Roman Numerals");
			String line;
			while ((line = reader.readLine()) != null) {
				Matcher m = p.matcher(line);
				StringBuffer converted = new StringBuffer(line.length());
				while (m.find()) {
					String chrNum = line.substring(m.start()+3, m.end());
					int arabic = Integer.parseInt(chrNum);
					String roman = RomanNumeral.int2roman(arabic);
					m.appendReplacement(converted, "chr"+roman);
				}
				m.appendTail(converted);
				
				writer.write(converted.toString());
				writer.newLine();
			}
		}
	}
	
	public static void main(String[] args) {
		new RomanNumeralize().instanceMain(args);
	}

}