import java.io.BufferedReader;
import java.util.Arrays;
import java.util.Collections;
import java.util.Scanner;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.io.LineNumberReader;

public class Test {

    public static String[] dnaArray = null;
    public static long start, stop;

    public static void main(String[] args) throws FileNotFoundException {

        int option = 0;

        do {
            option = menu();
        } while (option != 0);
        System.out.println(" DNA Management application end");
    }

    private static int menu() {
        System.out.println(" DNA Management application //\r\n" +
                "// 1 ? Read file //\r\n" +
                "// 2 ? Search pattern with alg1 //\r\n" +
                "// 3 ? Search pattern with alg2 //\r\n" +
                "// 4 ? Order sequence with alg1 //\r\n" +
                "// 5 ? Order sequence with alg2 //\r\n" +
                "// 0 ? Exit //\r\n" +
                "// Option? ");
        int choose;
        Scanner odczyt = new Scanner(System.in); //obiekt do odebrania danych od u?ytkownika

        choose = odczyt.nextInt();

        //String[] c=null;

        switch (choose) {
            case 1:
                try {
                    start = System.currentTimeMillis();
                    dnaArray = readFile("data.txt");
                    stop = System.currentTimeMillis();

                } catch (FileNotFoundException e) {
                    // TODO Auto-generated catch block
                    e.printStackTrace();
                }
                System.out.println(dnaArray[0]);
                break;
            case 2:
                Scanner enter = new Scanner(System.in);
                String xd = enter.nextLine();

                start = System.currentTimeMillis();
                System.out.println(countExists(xd, "data.txt"));
                stop = System.currentTimeMillis();
                break;
            case 3:
                try {
                    dnaArray = readFile("data.txt");

                } catch (FileNotFoundException e) {
                    // TODO Auto-generated catch block
                    e.printStackTrace();
                }


                System.out.println(dnaArray[0]);
                System.out.println("String to search?");
                Scanner enter2 = new Scanner(System.in);
                String xd2 = enter2.nextLine();

                start = System.currentTimeMillis();
                int count = sequentialSearch(dnaArray, xd2);
                stop = System.currentTimeMillis();
                System.out.println("found " + xd2 + " " + count);
                break;
            case 4:
                try {
                    dnaArray = readFile("data.txt");

                } catch (FileNotFoundException e) {
                    // TODO Auto-generated catch block
                    e.printStackTrace();
                }

                start = System.currentTimeMillis();
                Arrays.sort(dnaArray);
                stop = System.currentTimeMillis();

                for (String string : dnaArray) {
                    System.out.println(string);
                }

                break;
            case 5:
                try {
                    dnaArray = readFile("data.txt");

                } catch (FileNotFoundException e) {
                    // TODO Auto-generated catch block
                    e.printStackTrace();
                }

                start = System.currentTimeMillis();
                dnaArray = sortArrayOfStrings(dnaArray);
                stop = System.currentTimeMillis();

                for (String string : dnaArray) {
                    System.out.println(string);
                }

                break;
            default:
        }

        System.out.println("execute time (in millisec): "+(stop-start));

        return choose;
    }

    static int countExists(String targetString, String nazwaPliku) {
        File txt = new File(nazwaPliku);
        int count = 0;
        try {
            BufferedReader read = new BufferedReader(new FileReader(txt));
            String line;
            while ((line = read.readLine()) != null) {
                Matcher m = Pattern.compile(targetString).matcher(line);
                while (m.find()) {
                    count++;
                }
            }
            read.close();
        } catch (IOException e) {
            e.printStackTrace();
        }
        return count;
    }

    public static int sequentialSearch(String[] elements, String target) {


        if (elements == null)
            return -1;

        int count = 0;
        for (int j = 0; j < elements.length; j++) {
            if (elements[j] != null) {
                if (elements[j].contains(target)) {
                    count++;
                }
            }
        }
        return count;
    }

    public static String[] readFile(String csvFile) throws FileNotFoundException {
        File file = new File(csvFile);
        BufferedReader in = new BufferedReader(new FileReader(file));
        LineNumberReader lnr = new LineNumberReader(new FileReader(csvFile));
        String[] dna = null;

        int count = 0;
        String temp = "";

        try {
            lnr.skip(Long.MAX_VALUE);
            dna = new String[lnr.getLineNumber() + 1];
            lnr.close();


            while ((temp = in.readLine()) != null) {

                if (temp != null) {


                    dna[count] = temp;
                    count++;
                }
            }

            in.close();

        } catch (IOException e) {

            e.printStackTrace();
        }
       // Arrays.sort(dna);
        return dna;

    }

    public static void SearchAlg1(String[] x) {


        System.out.println(x);


    }

    public static String[] sortArrayOfStrings(String[] array) {
        for (int i = 1; i < array.length; i++) {
            String element = array[i];
            int j;
            for (j = i - 1; j >= 0 && element.compareTo(array[j]) <= 0; j--)
                array[j + 1] = array[j];

            array[j + 1] = element;
        }
        return array;
    }
}