What am I doing wrong?

I need help, I'm trying to create a program to Encipher words and phrases but it doesn't output what I want it to.
Heres the code

Code:

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import java.util.Scanner;
public class Cipher
{
  public static void main(String[] args)
    {
        Scanner keyboard = new Scanner(System.in);
        String Input;
        String Output = "";
        System.out.println("Input Word");
        String Encipher = keyboard.nextLine();
        Encipher.replaceAll("\\s","");
       
        Integer EncipherPosition = 0;
        String Cipher = "";
        for (EncipherPosition = 0; EncipherPosition < Encipher.length(); EncipherPosition ++)
            {
                char EncipherChar = Encipher.charAt(EncipherPosition);
                String EncipherString = "" + EncipherChar;
                boolean temp = Cipher.contains(EncipherString);
                if (temp == false)
                    {
                        Cipher += Encipher.charAt(EncipherPosition);
                    } 
            }
        System.out.println("This is what you Input: " + Cipher);
       
        String alphabet = "abcdefghijklmnopqrstuvwxyz";
        //sets the alphabet string
        Integer alphabetPosition = 0;
        for (alphabetPosition = 0;alphabetPosition < alphabet.length();alphabetPosition ++)
            {
                char alphabetTempChar = alphabet.charAt(alphabetPosition);
                String alphabetTempString = "" + alphabetTempChar;
                boolean alphabetTemp = Cipher.contains(alphabetTempString);
                if (alphabetTemp == false)
                    {
                        Cipher += alphabet.charAt(EncipherPosition);
                    }
            }
       
        System.out.println("This is your ciphered text" + Cipher + alphabet + Cipher);
        System.out.println("Input message:");
        Input = keyboard.nextLine();
       
        Integer position = 0;
        for (position = 0; position < alphabet.length(); position ++)
            {
                char CipherChar = Cipher.charAt(position);
                String CipherString = "" + CipherChar;
                char alphabetChar = alphabet.charAt(position);
                String alphabetString = "" + alphabetChar;
                Input.replace(alphabetString,CipherString);
            }
        System.out.println("This is your encoded message : " + Input);
        }
}

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And this is what it outputs if I enter "Testing" and "Testing one two three" when it asks for input

Code:

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Input Word
Testing
This is what you Input: Testing
This is your ciphered textTestinghhhhhhhhhhhhhhhhhhhabcdefghijklmnopqrstuvwxyzTestinghhhhhhhhhhhhhhhhhhh
Input message:
Testing one two three
This is your encoded message : Testing one two three

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User banned for one week for asking to pay others to do his homework for him. Cheating is not allowed on this forum.

Make that a permanent ban for trying to get around the original ban.