Template for Huffman Encoding in Java (some bugs may occur)

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package huffman;

import java.io.*;
import java.util.*;
import huffman.AbstractMap;
import static javafx.scene.input.KeyCode.V;

/**
 *
 * @author obobotette0
 */
public class Huffman {

    /**
     * @param args the command line arguments
     */
    public static void main(String[] args) throws FileNotFoundException, IOException {
        // TODO code application logic here
     
        //create variables
        System.out.println("Please enter the path and/or name of file");
        Scanner name = new Scanner(System.in);
        String file_name = name.nextLine();
        PrintWriter output = new PrintWriter(new FileWriter(new String("output.txt")));
        AbstractMap freq = new AbstractMap<>('0', 0);
        AbstractMap mix = new AbstractMap<>("null", 0);
        AbstractMap huffman = new AbstractMap<>("null", '0');
     
        char[] array;
        int nodes = 0;
        int min1, min2;
        File input = new File(file_name);
     
        Scanner read = new Scanner(input);
     
        //read each line and prse string
        while (read.hasNextLine()) {
            array = read.nextLine().replace(" ", "").replace("  ", "").replace("-", "").replace("!", "").replace(".", "").replace(",", "").replace("?", "").replace("/", "").replace(";", "").replace(":", "").replace("[", "").replace("]", "").toLowerCase().toCharArray();
         
            //for length of line
            //if key is found increase value as frequency
            //else its first instance
            for (int i = 0; i < array.length; i++) {
                if (freq.findIndex(array[i]) > -1) {
                    freq.input(array[i], freq.addFreq(array[i]) + 1);
                } else {
                    freq.input(array[i], 1);
                }
            }
        }
     
        //close reading
        read.close();

        //Print frequency table
        System.out.println("Printing frequency");
        output.append("Printing Frequency");
        output.println();
        freq.sort();      
        freq.print();
     
        output.append(freq.filePrint().toString());
        output.println();
        output.println();
     
        for (int i = 0; i < freq.size(); i++) {
            mix.input(freq.getKey(i).toString(), freq.getValue(i));
        }
     
        //while there is more than one node
        //begin combining
        while (mix.size() > 1) {
            //The first two nodes are combined with a binary value assigned as the key
            //The value is the sum of the frequencies
            mix.input(mix.mapping(mix.getKey(0), '0').toString() + " " + mix.mapping(mix.getKey(1), '1').toString(), mix.getValue(0) + mix.getValue(1));
            //Delete the first two nodes and resort list
            mix.remove(0);
            mix.remove(0);
            mix.sort();
         
        }
     
        //Print form of map
        System.out.println("Printing map");
        output.append("Printing map");
        output.println();
        mix.print();
     
        output.append(mix.filePrint().toString());
        output.println();
        output.println();
     
        //Parse the entire map into sections
        String[] chars = mix.getKey(0).split(" ");
     
        for (int a = 0; a < chars.length; a++) {
         
            //remove leading 0's and 1's from string
            array = "abcdefghijklmnopqrstuvwxyz".toCharArray();
            String c = chars[a].replace("0", "");
            c = c.replace("1", "");
            String[] temp;
            for (int b = 0; b < array.length; b++) {
             
                //separate binary from char
                temp = chars[a].split(c);
             
                //condition is true only if reduced string is a letter of the alphabet  
                if (c == null ? String.valueOf(array[b]) == null : c.equals(String.valueOf(array[b]))) {
                 
                    //input as binary key and char value
                    huffman.input(temp[0], c.charAt(0));
                }
            }
        }

        //Print binary map
        System.out.println("Printing binary");
        output.append("Printing binary");
        output.println();
     
        huffman.print();
        output.append(huffman.filePrint().toString());
        output.println();
        output.println();
     
        //Begin from top of file
        read = new Scanner(input);
     
        //Print encoded message
        System.out.println("Printing encoded message");
        output.append("Printing encoded message");
        output.println();
     
        while (read.hasNextLine()) {
            array = read.nextLine().replace(" ", "").toLowerCase().toCharArray();
            for (int i = 0; i < array.length; i++) {
                //return binary string for each found character
                if (huffman.findValue(String.valueOf(array[i]).charAt(0))) {
                    System.out.print(huffman.retValue(String.valueOf(array[i]).charAt(0)) + " ");
                    output.append(huffman.retValue(String.valueOf(array[i]).charAt(0)) + " ");
     
                }
            }
            System.out.println();
            output.println();
        }
     
        input = new File(new String("output.txt"));
     
        read = new Scanner(input);
        System.out.println("Printing decoded message");
        output.append("Printing decoded message");
        output.println();
        read.findInLine("Printing encoded message");
        while (read.hasNextLine()) {
            array = read.nextLine().replace(" ", "").toLowerCase().toCharArray();
            System.out.print(String.valueOf(array) + " " + array.length);
             
            for (int i = 0; i < array.length; i++) {
                 
                if (huffman.findKey(String.valueOf(array[i]))) {
                    //System.out.print(String.valueOf(array[i]) + " ");
                    System.out.print(huffman.retKey(String.valueOf(array[i])) + " ");
                    output.append(huffman.retKey(String.valueOf(array[i])) + " ");
     
                }
            }
            System.out.println();
            output.println();
        }
     
     
     
        output.flush();
     
    }
 
}