Books-Without-Borders/src/main/java/net/knarcraft/bookswithoutborders/GenenCrypt.java

package net.knarcraft.bookswithoutborders;

import java.util.Random;
import java.util.ArrayList;
import java.util.HashMap;

public class GenenCrypt {

	private final Random ranGen;
	private final String[] bases;
	private final ArrayList<String> originalCodonList;
	private final ArrayList<String> shuffledCodonList;
	private final String[] charList;
	private final HashMap<String,String[]> codonTable;
	private final HashMap<String, String> decryptTable;
	private final String key;
	
	public GenenCrypt(String key){
		
		// define the initial, unshuffled codon list of 4 base codons
		originalCodonList = new ArrayList<>();
		bases = new String[]{"A", "T", "G", "C"};
		for(int i = 0; i < 4; i++){ 
			for(int j = 0; j < 4; j++){
				for(int k = 0; k < 4; k++){
					for(int l = 0; l < 4; l++){
						originalCodonList.add("" + bases[i] + bases[j] + bases[k] + bases[l]);
					}
				}
			}
		}
		
		// make a random number generator with a seed based on the key
		this.key = key;
		long longKey = 0;
		for(int i = 0; i < key.length(); i++){
			longKey += (int)key.charAt(i);
		}
		ranGen = new java.util.Random(longKey);
		
		// use the random number generator and the originalCodonList to make a shuffled list
		shuffledCodonList = new ArrayList<>();
		while(originalCodonList.size() > 0){
			int index = ranGen.nextInt(originalCodonList.size());
			shuffledCodonList.add(originalCodonList.get(index));
			originalCodonList.remove(index);
		}
		
		// define the characters that can be encoded, 64 in total
		// 26 capital letters
		// 10 digits
		// space, newline, and tab
		// the symbols . , ? " ! @ # $ % ^ & * ( ) - + = / _ \ : ; < >
		charList = new String[]{"A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K", "L", "M", "N", "O", "P", "Q", "R", "S", "T", "U", "V", "W", "X", "Y", "Z", "0", "1", "2", "3", "4", "5", "6", "7", "8", "9", " ", "\t", "\n", ".", ",", "?", "\"", "!", "@", "#", "$", "%", "^", "&", "*", "(", ")", "-", "+", "=", "/", "_", "\\", ":", ";", "<", ">", "|"};
		
		// define the codon table to encode text
		codonTable = new HashMap<>();
		for(int i = 0; i < charList.length; i++){
			String[] tempArray = new String[]{shuffledCodonList.get(4 * i), shuffledCodonList.get(4 * i + 1), shuffledCodonList.get(4 * i + 2), shuffledCodonList.get(4 * i + 3)};
			//System.out.println(i);
			codonTable.put(charList[i], tempArray);
		}
		
		// define the decryption table
		decryptTable = new HashMap<>();
		for(int i = 0; i < codonTable.size(); i++){
			String s = charList[i];
			String[] sa = codonTable.get(s);
			decryptTable.put(sa[0], s);
			decryptTable.put(sa[1], s);
			decryptTable.put(sa[2], s);
			decryptTable.put(sa[3], s);
		}
		
		
	}
		
	public void printShuffledList(){
		for (String s : shuffledCodonList) {
			System.out.println(s);
		}
	}
	public void printOriginalList(){
		for (String s : originalCodonList) {
			System.out.println(s);
		}
	}
	public void printCodonTable(){
		// print the codon table
		for(int i = 0; i < codonTable.size(); i++){
			String s = charList[i];
			String[] sa = codonTable.get(s);
			switch (s) {
				case "\t":
					System.out.println(i + "\t" + "\\t" + "\t" + sa[0] + ", " + sa[1] + ", " + sa[2] + ", " + sa[3]);
					break;
				case "\n":
					System.out.println(i + "\t" + "\\n" + "\t" + sa[0] + ", " + sa[1] + ", " + sa[2] + ", " + sa[3]);
					break;
				case " ":
					System.out.println(i + "\t" + "\" \"" + "\t" + sa[0] + ", " + sa[1] + ", " + sa[2] + ", " + sa[3]);
					break;
				default:
					System.out.println(i + "\t" + s + "\t" + sa[0] + ", " + sa[1] + ", " + sa[2] + ", " + sa[3]);
					break;
			}
		}
	}
	
	public String encrypt(String input){
		StringBuilder output = new StringBuilder();
		for(int i = 0; i < input.length(); i++){
			// insert junk bases
			int offset  = key.charAt(i % key.length());
			StringBuilder junk = new StringBuilder();
			for(int j = 0; j < offset; j++){
				junk.append(bases[ranGen.nextInt(4)]);
			}
			output.append(junk);
			int choose = ranGen.nextInt(4);
			String s = ("" + input.charAt(i)).toUpperCase();
			if(codonTable.containsKey(s)){
				String[] sa = codonTable.get(s);
				output.append(sa[choose]);
			}
		}
		// add some junk bases to the end of the cipher text
		int offset = key.charAt(input.length() % key.length());
		StringBuilder junk = new StringBuilder();
		for(int j = 0; j < offset; j++){
			junk.append(bases[ranGen.nextInt(4)]);
		}
		output.append(junk);
		return output.toString();
	}
	
	public String decrypt(String in){
		String input = "" + in;
		StringBuilder output = new StringBuilder();
		int keyCount = 0;
		int junk = key.charAt(keyCount % key.length());
		while(input.length() > junk){
			// cuts out the junk bases
			input = input.substring(junk);
			// get the codon, decrypt the codon, remove it from the input string
			String codon = input.substring(0, 4);
			output.append(decryptTable.get(codon));
			input = input.substring(4);
			// increment the key counter and update junk
			keyCount++;
			junk = key.charAt(keyCount % key.length());
		}
		return output.toString();
	}
	
	/*public static void main(String[] args){
		GenenCrypt gc = new GenenCrypt("Another Key");
		gc.printCodonTable();
		System.out.println();
		System.out.println();
		System.out.println();
		System.out.println("Encrypting the line \"Hello World!\"");
		String encrypted = gc.encrypt("Hello World!");
		System.out.println(encrypted);
		System.out.println();
		System.out.println("Decrypting the ciphertext");
		System.out.println(gc.decrypt(encrypted));
		
	}*/
}