import java.util.*;
import java.io.*;
/**
*This program converts rna to dna & vice versa
*/
public class DNAtoRNA {
    /**
    *This main method gets user input
    *and calls method the other methods
    *@param args main method arguments
    */
    public static void main(String[] args) {
        Scanner console = new Scanner(System.in);

        boolean toRNA = true;

        System.out.println("                Welcome to the RNA to DNA Converter");
        System.out.println("You may enter R to convert DNA sequences " +
            "to RNA, D to convert RNA sequences to DNA,");
        System.out.println("or Q to quit, and names of the input " +
            "and output files for each conversion. Each line ");
        System.out.println("of the file contains a single sequence " +
            "followed by 0 or more mutation positions.");
        System.out.println();
        boolean isValid = false;

        while (!isValid) {
            System.out.print("Enter R (convert to RNA), D (convert to DNA), or q (quit): ");
            String letterInput = console.next();
            if (letterInput.equalsIgnoreCase("R")) {
                toRNA = true;
                isValid = true;
            }
            if (letterInput.equalsIgnoreCase("D")) {
                toRNA = false;
                isValid = true;
            }
            if (letterInput.equalsIgnoreCase("Q")) {
                isValid = true;
                System.exit(1);
            }
            if (letterInput.length() > 1) {
                isValid = false;
            }

        }
        PrintStream output = null;
        Scanner input = null;
        processFile(toRNA, input, output);
    }
    /**
    *Takes a file as input from
    *the user
    *@param console console that accepts input
    *@return returns the input when called
    */
    public static Scanner getInputScanner(Scanner console) {
        Scanner input = null;
        while (input == null) {
            System.out.print("Enter input file: ");
            String inputName = console.next();
            try {
                input = new Scanner(new File(inputName));
            } catch (FileNotFoundException e) {
                System.out.println("Problem Creating file, try again.");
            }
        }
        return input;
    }
    /**
    *Creates a new file
    *for the output
    *@param console console that accepts input
    *@return returns the output when called
    */
    public static PrintStream getOutputPrintStream(Scanner console) {
        PrintStream output = null;
        while (output == null) {
            System.out.print("Enter output file: ");
            String outputName = console.next();
            try {
                output = new PrintStream(new File(outputName));
            } catch (FileNotFoundException e) {
                System.out.println("File not found. Please try again.");
            }
        }
        return output;
    }

    /**
    *processes the file
    *puts the dna and rna lines
    *in to a line that is passed
    *to the convert methods
    *Then calls the convert methods
    *and presents the result
    *@param toRNA boolean that decides how to convert
    *@param input scanner that takes input
    *@param output printstream thats prints to a new file
    */
    public static void processFile(boolean toRNA, Scanner input, PrintStream output) {
        Scanner console = new Scanner(System.in);
        input = getInputScanner(console);
        output = getOutputPrintStream(console);

        while (input.hasNext()) {
            String line = input.nextLine();

            String toBePrinted = "";
            if (toRNA == true) {
                toBePrinted = convertToRNA(line);
                System.out.print(" ");
            } else {
                toBePrinted = convertToDNA(line);
            }
            output.println(toBePrinted);
        }
    }

    /**
    *converts the input
    *to rna
    *@param line string that contains input
    *@return returns the converted RNA
    */
    public static String convertToRNA(String line) {
        String conversion = "";
        Scanner scan = new Scanner(line);

        String n = scan.next();



        for (int i = 0; i < n.length(); i++) {
            if (n.charAt(i) == ('A')) {
                conversion += "U";
            } else if (n.charAt(i) == 'T') {
                conversion += "A";
            } else if (n.charAt(i) == 'C') {
                conversion += "G";
            } else if (n.charAt(i) == 'G') {
                conversion += "C";
            }
            else {
                throw new IllegalArgumentException();
            }
        }

        while (scan.hasNext()) {
            n = scan.next();
            int mutation;
            try {
                mutation = Integer.parseInt(n);
            } catch (NumberFormatException e) {
                throw new IllegalArgumentException();
            }

            if (conversion.length() > mutation + 1) {
                if (conversion.charAt(mutation) == 'U') {
                    conversion = conversion.substring(0, mutation)
                        + "C" + conversion.substring(mutation + 1);
                } else if (conversion.charAt(mutation) == 'A') {
                    conversion = conversion.substring(0, mutation) +
                        "G" + conversion.substring(mutation + 1);
                } else if (conversion.charAt(mutation) == 'G') {
                    conversion = conversion.substring(0, mutation)
                        + "U" + conversion.substring(mutation + 1);
                } else if (conversion.charAt(mutation) == 'C') {
                    conversion = conversion.substring(0, mutation)
                        + "A" + conversion.substring(mutation + 1);
                }
            } else if (conversion.length() == mutation + 1) {
                if (conversion.charAt(mutation) == 'U') {
                    conversion = conversion.substring(0, mutation) + "C";
                } else if (conversion.charAt(mutation) == 'A') {
                    conversion = conversion.substring(0, mutation) + "G";
                } else if (conversion.charAt(mutation) == 'G') {
                    conversion = conversion.substring(0, mutation) + "U";
                } else if (conversion.charAt(mutation) == 'C') {
                    conversion = conversion.substring(0, mutation) + "A";
                }
                else {
                    throw new IllegalArgumentException();
                }
            }
            conversion += " " + mutation;
        }
        scan.close();
        return conversion;
    }

    /**
    *converts input to dna
    *@param line line thats contains input
    *@return returns the converted DNAtoRNA
    */
    public static String convertToDNA(String line) {
        String conversion = "";
        Scanner scan = new Scanner(line);

        String n = scan.next();
        for (int i = 0; i < n.length(); i++) {
            if (n.charAt(i) == ('U')) {
                conversion += "A";
            } else if (n.charAt(i) == 'A') {
                conversion += "T";
            } else if (n.charAt(i) == 'G') {
                conversion += "C";
            } else if (n.charAt(i) == 'C') {
                conversion += "G";
            }
            else {
                throw new IllegalArgumentException();
            }
        }

        while (scan.hasNext()) {
            n = scan.next();
            int mutation;
            try {
                mutation = Integer.parseInt(n);
            } catch (NumberFormatException e) {
                throw new IllegalArgumentException();
            }
            if (conversion.length() > mutation + 1) {
                if (conversion.charAt(mutation) == 'C') {
                    conversion = conversion.substring(0, mutation)
                        + "T" + conversion.substring(mutation + 1);
                } else if (conversion.charAt(mutation) == 'G') {
                    conversion = conversion.substring(0, mutation)
                        + "A" + conversion.substring(mutation + 1);
                } else if (conversion.charAt(mutation) == 'A') {
                    conversion = conversion.substring(0, mutation)
                        + "C" + conversion.substring(mutation + 1);
                } else if (conversion.charAt(mutation) == 'T') {
                    conversion = conversion.substring(0, mutation)
                        + "G" + conversion.substring(mutation + 1);
                }
            } else if(conversion.length() == mutation + 1){
                if (conversion.charAt(mutation) == 'C') {
                    conversion = conversion.substring(0, mutation) + "T";
                } else if (conversion.charAt(mutation) == 'G') {
                    conversion = conversion.substring(0, mutation) + "A";
                } else if (conversion.charAt(mutation) == 'A') {
                    conversion = conversion.substring(0, mutation) + "C";
                } else if (conversion.charAt(mutation) == 'T') {
                    conversion = conversion.substring(0, mutation) + "G";
                }
                else {
                    throw new IllegalArgumentException();
                }
            }
            conversion += " " + mutation;
        }
        scan.close();
        return conversion;
    }
}