I would like to replace a parts of string with another string

I am just starting and I have created parts of my code, part a finds the int location of the letter(or phrase)that the user is looking for in the Master string(which is line in the code). Part b counts how many times the letter(or phrase appears). In the next part(WITH OUT CREATING A NEW METHOD) I want if s(what the user is looking) is a "_" to replace them with something else like "-" for instance, and then print it out.
here is my code:

import java.util.Scanner;
import java.util.concurrent.CountDownLatch;
public class Main
{
//my code acomplishes the goal but it dose not do it the way you are asking for, sorry:(
public static String line; // The line to format
public static void main(String [] arrrgs)
{
Scanner input = new Scanner(System.in);
System.out.println("Enter a master String:");
String line = input.nextLine();
System.out.println("Enter a letter to look for:");
String s = input.nextLine();
System.out.println("Enter a starting location:");
int begin = input.nextInt();
//part a
int loc = begin;
while (loc != line.length()){
loc++; 
if (loc != line.length()){
if (s.matches(line.substring(loc, loc + 1))){
System.out.println(s + " appears at " + (loc + 1));//prints location of strin except for first one
}
}   
}
int oomf = 1;
if(s.matches(line.substring(0, 1)))//looks at first letter
System.out.println(oomf); //prints if nesasary
//part b
int count = 0;
int timer = begin;
while (timer != line.length()){
timer++; 
if (timer != line.length()){
if (s.matches(line.substring(timer, timer + 1))){
count++;
}
}   
}
System.out.println(s +"apears " + count + " times.");
}
}

As you see from the comments there is JAVA API to manipulate strings.

Here you are an example how to do it.

public static void main(String[] args) {
String testString = "Hello _ World _";
// Replace with Java API:
System.out.println(testString.replace('_', '-'));
// Replace using own naive code:
String newString = "";
for(int i = 0; i < testString.length(); i++) {
if(testString.charAt(i) == '_') {
newString += "-";
} else {
newString += testString.charAt(i);
}
}
System.out.println(newString);
}

You should be able to adopt this to your program.

Please note that in java all strings are immutable. That means, that you can't change an string once it is created. So you have to create new strings with your changes.

This is why you have to work with the return value of replace(). Your original String will remain the same.