Fixed sonarqube findings

src/main/java/com/mattrixwv/cipherstream/monosubstitution/Autokey.java

@@ -0,0 +1,110 @@
+//CipherStreamJava/src/main/java/com/mattrixwv/CipherStreamJava/Autokey.java
+//Mattrixwv
+// Created: 07-25-21
+//Modified: 07-03-22
+package com.mattrixwv.cipherstream.monosubstitution;
+
+
+import com.mattrixwv.cipherstream.exceptions.InvalidInputException;
+import com.mattrixwv.cipherstream.exceptions.InvalidKeywordException;
+
+
+public class Autokey extends Vigenere{
+	//Special rules for setting the strings for encoding
+	private void encodeSet(String keyword, String inputString) throws InvalidKeywordException, InvalidInputException{
+		//Set the input
+		setInputString(inputString);
+
+		StringBuilder newKey = new StringBuilder();
+		//Remove all unneccessary elements from the key
+		setKeyword(keyword);
+		newKey.append(keyword);
+		//Remove all unneccessary elements from the input
+		setKeyword(inputString);
+		newKey.append(getKeyword());
+
+		//Make sure the key is not any longer than the input
+		keyword = newKey.substring(0, getKeyword().length());
+
+		//Set the new keyword
+		setKeyword(keyword);
+		//Make sure to update the offset
+		offset.clear();
+		setOffset();
+	}
+	//Setting the strings for decoding
+	private void decodeSet(String keyword, String inputString) throws InvalidKeywordException, InvalidInputException{
+		//Remove all unneccessary elements from the key
+		setKeyword(keyword);
+		//Remove all unneccessary elements from the input
+		setInputString(inputString);
+	}
+	//Decodes the inputString
+	@Override
+	protected String decode(){
+		//Decode what the key will allow, add that to the key and continue
+		StringBuilder currentOutput = new StringBuilder();
+		StringBuilder fullOutput = new StringBuilder();
+
+		//Step through every character in the inputString and advance it the correct amount, according to offset
+		int offsetCnt = 0;
+		for(int letterCnt = 0;letterCnt < inputString.length();++letterCnt){
+			//If we have reached the end of the keyword add what we have to it and continue
+			if(offsetCnt == keyword.length()){
+				setKeyword(keyword + currentOutput.toString());
+				fullOutput.append(currentOutput);
+				currentOutput = new StringBuilder();
+			}
+
+			char letter = inputString.charAt(letterCnt);
+			if(Character.isUpperCase(letter)){
+				letter -= offset.get((offsetCnt++) % offset.size());
+				if(letter < 'A'){
+					letter += 26;
+				}
+				else if(letter > 'Z'){
+					letter -= 26;
+				}
+			}
+			else if(Character.isLowerCase(letter)){
+				letter -= offset.get((offsetCnt++) % offset.size());
+				if(letter < 'a'){
+					letter += 26;
+				}
+				else if(letter > 'z'){
+					letter -= 26;
+				}
+			}
+			currentOutput.append(letter);
+		}
+		//Empty the last character that were decoded
+		fullOutput.append(currentOutput);
+
+		//Save and return the results
+		outputString = fullOutput.toString();
+		return outputString;
+	}
+
+
+	//Constructor
+	public Autokey(){
+		super();
+	}
+	public Autokey(boolean preserveCapitals, boolean preserveWhitespace, boolean preserveSymbols){
+		super(preserveCapitals, preserveWhitespace, preserveSymbols);
+	}
+	//Encodes inputString using the Autokey cipher
+	@Override
+	public String encode(String keyword, String inputString) throws InvalidKeywordException, InvalidInputException{
+		reset();
+		encodeSet(keyword, inputString);
+		return encode();
+	}
+	//Decodes inputString using the Autokey cipher
+	@Override
+	public String decode(String keyword, String inputString) throws InvalidKeywordException, InvalidInputException{
+		reset();
+		decodeSet(keyword, inputString);
+		return decode();
+	}
+}