package middlewares;

import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileWriter;
import java.io.IOException;
import java.net.URL;
import java.util.ArrayList;
import java.util.Scanner;

import datastructures.ReducedReadLine;
import datastructures.TargetLine;
import exceptions.ChromosomeFormatException;
import exceptions.ChromosomeNotFoundException;
import exceptions.NullOrNegativeRangeException;
import exceptions.RangeFormatException;
import exceptions.RangeLimitNotFoundException;

/**
 * Miscellaneous methods for different uses.
 * 
 * @author Ali Abdallah
 * @version 01.2011
 * @since jdk 1.6.0
 */
public class Misc {

	/**
	 * Make the first letter big, if possible. nGSrich -> NGSrich.
	 * 
	 * @param s the string
	 * @return the same string with the first letter big.
	 */
	public static String bigFirst(String s) {
		return s.substring(0, 1).toUpperCase() + s.substring(1);
	}

	/**
	 * Creates a shortcut for the file with a different file extension.
	 * 
	 * @param fName the original file name.
	 * @param newExt the new extension of the file.
	 * @param dir the directory of the mad link.
	 * @return a link to the file fName with a different extension.
	 */
	public static File rename(String fName, String newExt, String dir) {

		String inDirShortCut = dir + Misc.slash(dir);
		String fShortcutName = inDirShortCut + Misc.prefix(fName) + "."
				+ newExt;
		Runtime r = Runtime.getRuntime();
		try {
			r.exec("ln -s " + fName + " " + fShortcutName);
		} catch (IOException e) {
			e.printStackTrace();
		}
		try {
			Thread.sleep(100);
		} catch (InterruptedException e) {
			e.printStackTrace();
		}
		return new File(fShortcutName);
	}

	/**
	 * @return the path of the bin directory of this software.
	 */
	public static String binDir() {
		URL url = new Misc().getClass().getResource("Misc.class");
		String path = url.toString().substring(url.toString().indexOf(":") + 1);
		path = path.substring(0, path.lastIndexOf("/"));

		return path.substring(0, path.lastIndexOf("/"));

	}
	
	/**
	 * @return the path of this software.
	 */
	public static String scriptDir() {
		URL url = new Misc().getClass().getResource("../NGSrich.class");
		String path = url.toString().substring(url.toString().indexOf(":") + 1);
		path = path.substring(0, path.lastIndexOf("/"));
		return path.substring(0, path.lastIndexOf("/")+1);

	}
	
	public static void main(String[] args) {
		System.out.println(scriptDir());
	}

	/**
	 * @param path 
	 * @return extends the path by a slash at the end, in the case it don't 
	 * exists.
	 */
	public static String slash(String path) {
		return (path.endsWith("/") ? "" : "/");
	}

	/**
	 * @return the name of the host.
	 */
	public static String getHostName() {
		Runtime rt = Runtime.getRuntime();
		String erg = "";
		try {
			File f = new File("hostname.sh");
			FileWriter fw = new FileWriter(f);

			fw.write("#!/bin/bash\r\nproc=$(hostname -s).$$\r\necho $proc");
			fw.close();
			Process p = rt.exec("chmod 700 " + f.getAbsolutePath());
			p = rt.exec("sh " + f.getAbsolutePath());

			Scanner s = new Scanner(p.getInputStream());

			while (s.hasNextLine()) {
				erg += (s.nextLine());
			}
			s.close();

			f.delete();
		} catch (IOException e) {
			e.printStackTrace();
		}
		return erg;
	}

	/**
	 * @param fileName
	 * @return the extension of the file.
	 */
	public static String suffix(String fileName) {
		return fileName.substring(fileName.lastIndexOf(".") + 1);
	}

	/**
	 * @param fileName
	 * @return the name of the file without the extension.
	 */
	public static String prefix(String fileName) {
		return fileName.substring(fileName.lastIndexOf("/") + 1,
				fileName.lastIndexOf("."));
	}

	/**
	 * @param fileName
	 * @return the directory of the specified file.
	 */
	public static String path(String fileName) {
		String absolutePath = 
						new File(fileName).getParentFile().getAbsolutePath();
		return absolutePath+slash(absolutePath);
	}

	/**
	 * Check if the chromosome names in the target file are a subset of the
	 * chromosome name in the alignment file.
	 * 
	 * @param alignment the alignment file.
	 * @param target the target file.
	 * @return true if target chromosomes are a subset of alignment chromosome
	 * and false otherwise.
	 */
	public static boolean areChromosomeCompatible(File alignment, File target){
		Scanner aScan = null, tScan = null;
		try {
			aScan = new Scanner(alignment);
			tScan = new Scanner(target);
			
			ArrayList<String> alist = new ArrayList<String>();
			ArrayList<String> tlist = new ArrayList<String>();
			while(aScan.hasNextLine()){
				ReducedReadLine rl = new ReducedReadLine(aScan.nextLine());
				if(alist.indexOf(rl.chrom())==-1)
					alist.add(rl.chrom());
			}
			while(tScan.hasNextLine()){
				TargetLine tl = new TargetLine(tScan.nextLine());
				if(tlist.indexOf(tl.chrom())==-1)
					tlist.add(tl.chrom());
			}
			for(int i = 0; i < tlist.size(); i++){
				if(alist.indexOf(tlist.get(i))!=-1)
					return true;
			}			
		} catch (FileNotFoundException e) {	
			e.printStackTrace();
		} catch (ChromosomeFormatException e) {
			e.printStackTrace();
		} catch (ChromosomeNotFoundException e) {
			e.printStackTrace();
		} catch (RangeFormatException e) {
			e.printStackTrace();
		} catch (RangeLimitNotFoundException e) {
			e.printStackTrace();
		} catch (NullOrNegativeRangeException e) {
			e.printStackTrace();
		}


		return false;
	}
	
}