Main.java

import java.util.Objects;
import java.util.Scanner;
import java.util.ArrayList;
import java.util.concurrent.TimeUnit;

public class Main {

    public static void main(String[] args) throws InterruptedException {
        // Initialize an ArrayList to store DNA sequences
        ArrayList<String> sequences = new ArrayList<>();

        // Read the DNA sequences from file
        sequences = Reader.readFile();

        // Ask the user which sequences to compare
        Scanner sc = new Scanner(System.in);

        // Display welcome screen
        Display.clear();

        // Initialisation of the menu
        boolean exit = false;
        String option = "";
        int indexSequence1 = -1, indexSequence2 = -1;

        // Start the principal loop
        System.out.println("\nWhen you want to choose an option please put the number associate");
        do {
            option = "";
            if (sequences.size() == 0) {
                System.out.print("You got different options:\n");
                System.out.print(Const.black);
                System.out.print("1- Use 2 sequences of the file\n");
                System.out.print("2- Use 1 sequence from the file and 1 of your own creation\n");
                System.out.print(Const.white + "3- Use 2 sequences from your creation\n");
                System.out.print(Const.black + "4- See the file\n5- Add a sequence to the file\n");
                System.out.print(Const.white + "6- Exit\n\n>");
                if (sc.hasNextInt()) {
                    option = sc.nextLine();
                    if (Objects.equals(option, "1") || Objects.equals(option, "2") || Objects.equals(option, "4")
                            || Objects.equals(option, "5")) {
                        System.out.print(Const.colors[5] + "Option unavailable as file not found\n" + Const.white);
                        TimeUnit.SECONDS.sleep(2);
                    } else if (Objects.equals(option, "3") || Objects.equals(option, "6")) {
                    } else {
                        System.out.print(Const.white + "Please enter an int from 1 to 6\n>");
                    }
                } else {
                    System.out.print(Const.white + "Please enter an int from 1 to 6\n>");
                }
            } else {
                System.out.print(
                        "\nYou got different options:\n1- Use 2 sequences of the file\n2- Use 1 sequence from the file and 1 of your own creation\n3- Use 2 sequences from your creation\n4- See the file\n5- Add a sequence to the file\n6- Exit\n\n>");
                option = sc.nextLine();
            }

            // condition to leave the principal loop
            if (Objects.equals(option, "6")) {
                exit = true;
            }
            Display.clear();

            // The option of taking two sequences of the bank
            if (Objects.equals(option, "1") && sequences.size() != 0) {
                Display.clear();
                System.out.print("Choose the sequences you want from the file:\n");

                // Display the sequences to let choose the user
                Display.bank_sequence(sequences);

                do {
                    System.out.print("First one:\n>");
                    indexSequence1 = getIndexSequence(sequences, sc, indexSequence1);
                    System.out.print("Second one:\n>");
                    indexSequence2 = getIndexSequence(sequences, sc, indexSequence2);
                } while (indexSequence1 > 10 && indexSequence2 > 10);
                Display.scanning();
                Display.clear();
                System.out.printf(Const.white + "\nYou chose sequences %s and %s\n\n", sequences.get(indexSequence1),
                        sequences.get(indexSequence2));
                // Run the Smith-Waterman algorithm on two sequences and print the result
                int score = Algorithms.SmithWatermanAlgorithm(sequences.get(indexSequence1),
                        sequences.get(indexSequence2),
                        new int[sequences.get(indexSequence1).length() + 1][sequences.get(indexSequence2).length() + 1],
                        1, 0, -2);
                System.out.println("The final score is " + score);
                Display.waiting();
                String trash = sc.nextLine();
                trash = sc.nextLine();
            }

            // The option of taking one sequence of the bank and create one
            if (Objects.equals(option, "2") && sequences.size() != 0) {

                // Display the sequences
                Display.bank_sequence(sequences);

                System.out.print("Choose the sequence you want from the file:\n>");
                // Choice of the one of the bank
                do {
                    indexSequence1 = getIndexSequence(sequences, sc, indexSequence1);
                } while (indexSequence1 > 10);

                // Creation of the user's sequence
                String trash = sc.nextLine();
                String newSequence;
                int temp = 0;
                do { // Do the security for the DNA letters
                    System.out.printf(
                            Const.white
                                    + "Please write your own second sequence (is only available with : A,C,G,T)\n>");
                    newSequence = sc.nextLine();
                    temp = sequence(newSequence);
                } while (temp != 1);

                // short waiting screen to make a little suspense
                Display.scanning();
                Display.clear();
                System.out.printf(Const.white + "\nYou chose sequences %s and %s\n\n", sequences.get(indexSequence1),
                        newSequence);
                int score = Algorithms.SmithWatermanAlgorithm(sequences.get(indexSequence1), newSequence,
                        new int[sequences.get(indexSequence1).length() + 1][newSequence.length() + 1], 1, 0, -2);
                System.out.println("The final score is " + score);
                Display.waiting();
                trash = sc.nextLine();
            }

            // The option of creating two sequences
            if (Objects.equals(option, "3")) {

                String newSequence1;
                int temp = 0;
                do {
                    System.out.printf(
                            Const.white + "Please write your own first sequence (is only available with : A,C,G,T)\n>");
                    newSequence1 = sc.nextLine();
                    temp = sequence(newSequence1);
                } while (temp != 1);

                String newSequence2;
                temp = 0;
                do {
                    System.out.printf(
                            Const.white
                                    + "Please write your own second sequence (is only available with : A,C,G,T)\n>");
                    newSequence2 = sc.nextLine();
                    temp = sequence(newSequence2);
                } while (temp != 1);

                // short waiting screen to make a little suspense
                Display.scanning();
                Display.clear();
                System.out.printf(Const.white + "\nYou chose sequences %s and %s\n\n", newSequence1, newSequence2);
                int score = Algorithms.SmithWatermanAlgorithm(newSequence1, newSequence2,
                        new int[newSequence1.length() + 1][newSequence2.length() + 1], 1, 0, -2);
                System.out.println("The final score is " + score);
                Display.waiting();
                String trash = sc.nextLine();
            }

            // The option of just display sequences
            if (Objects.equals(option, "4") && sequences.size() != 0) {
                Display.bank_sequence(sequences);
            }

            if (Objects.equals(option, "5") && sequences.size() != 0) {
                String newSequence1;
                int temp = 0;
                do {
                    System.out.printf(
                            Const.white + "Please write your own sequence (is only available with : A,C,G,T)\n>");
                    newSequence1 = sc.nextLine();
                    temp = sequence(newSequence1);
                } while (temp != 1);
                Write.write(newSequence1);

                // Read again the DNA sequences from file with the new sequence added
                sequences = Reader.readFile();
            }

        } while (exit != true);
        System.out.println("Thank you see you later");
        sc.close();
    }

    private static int sequence(String newSequence) {
        int pass = 0;
        for (int i = 0; i < newSequence.length(); i++) {
            if (newSequence.charAt(i) == 'A' || newSequence.charAt(i) == 'C' || newSequence.charAt(i) == 'G'
                    || newSequence.charAt(i) == 'T') {
                pass += 1;
            } else {
                pass = 0;
            }
        }
        if (pass == newSequence.length()) {
            return 1;
        }
        return 0;
    }

    // This function gets the index of the sequence
    private static int getIndexSequence(ArrayList<String> sequences, Scanner sc, int indexSequence) {
        do {
            if (sc.hasNextInt()) {
                indexSequence = sc.nextInt() - 1; // Convert from 1-based to 0-based index. Due to the start at 0 in
                                                  // java in an array
                if ((indexSequence < 0 || indexSequence >= sequences.size()) && indexSequence != 10) {
                    System.out.printf(Const.white + "Please enter an int from %d to %d\n>", 1, sequences.size());
                }
            } else {
                System.out.printf(Const.white + "Please enter an int from %d to %d\n>", 1, sequences.size());
                sc.next(); // Clear the scanner buffer
            }
        } while ((indexSequence < 0 || indexSequence >= sequences.size()) && indexSequence != 10);
        return indexSequence;
    }
}