Global sequence alignment

Question

I need to align two DNA sequences (they are strings). The matching characters have to be aligned with a vertical line | and the mismatches with a space. Here is my code, the whole thing works well I just can't seem to find a way to align the strings.

//Variable List
Scanner keyboard = new Scanner(System.in);
String s_one, s_two, aligner = " ";
int len_one = 0, len_two = 0, a = 0, total_pos = 0, total_neg = 0, total_score = 0;
char char_one = ' ', char_two = ' ', compare = ' ';
//End Variable List

System.out.println("Enter the first DNA sequence: ");
s_one = keyboard.next().toUpperCase();
System.out.println("Enter the second DNA sequence: ");
s_two = keyboard.next().toUpperCase();

len_one = s_one.length();
len_two = s_two.length();

while(len_one > a && len_two > a){
    char_one = s_one.charAt(a);
    char_two = s_two.charAt(a);
    a++;
    if(char_one == char_two){
        total_pos += 2;
        aligner = "|";
        System.out.println(aligner);
    }else if(char_one != char_two){
        total_neg -= 1;
        aligner = " ";
        System.out.println(aligner);
    }
}

//Output
total_score = total_pos + total_neg;
System.out.println(s_one);
System.out.println(s_two);
System.out.println("The total score is: " + total_score);

do{//Ask the user if they want to re-enter another DNA sequence
    System.out.println("Would you like to re-enter another DNA sequence? Y/N");
    compare = keyboard.next().charAt(0);
    if(compare == 'y' || compare == 'Y'){

        System.out.println("Enter the first DNA sequence: ");
        s_one = keyboard.next().toUpperCase();
        System.out.println("Enter the second DNA sequence: ");
        s_two = keyboard.next().toUpperCase();

        len_one = s_one.length();
        len_two = s_two.length();

        while(len_one > a && len_two > a){
            char_one = s_one.charAt(a);
            char_two = s_two.charAt(a);
            a++;
            if(char_one == char_two){
                total_pos += 2;
            }else if(char_one != char_two){
                total_neg -= 1;
            }
        }

        //Output
        total_score = total_pos + total_neg;
        System.out.println(s_one);
        System.out.println();
        System.out.println(s_two);
        System.out.println("The total score is: " + total_score);
    }
}while(compare == 'y' || compare == 'Y');
System.out.println("Thank You!");

Lets say we have string 1 = ABBABB and string 2 = ABAAAB, I need the whole output to look like this:

ABBABB
|| | |
ABAAAB
The total score is: 6

I just don't know how to get the vertical lines to get into the right place.

Answer 1

Update:

I looks like you just need to print the aligner between your other two print statments for s_one and s_two.

System.out.println(s_one);
System.out.println(aligner);
System.out.println(s_two);

It looks like there is debugging output in you alignment loop. You need to remove those println statements to avoid a bunch a "garbage" at the top your output. Also make sure you append to both aligners...

  if(char_one == char_two){
    total_pos += 2;
    aligner += "|";
  }else if(char_one != char_two){
    total_neg -= 1;
    aligner += " ";
  }
}

Answer 2

To get your current code to work.

   System.out.println(s_one);
    while(len_one > a && len_two > a){
        char_one = s_one.charAt(a);
        char_two = s_two.charAt(a);
        a++;
        if(char_one == char_two){
            total_pos += 2;
            aligner = "|";
            System.out.print(aligner);
        }else if(char_one != char_two){
            total_neg -= 1;
            aligner = " ";
            System.out.print(aligner);
        }
    }
    System.out.println();
    System.out.println(s_two);

Possibly a better answer.

StringBuilder alignment = new StringBuilder();

for (int i = 0; i < s_one.length(); i++) {
   if (s_one.chatAt(i) == s_two.charAt(i)) {
      alignment.append("|");
   } else {
      alignment.append(" ");
   }
}

//at the end

System.out.println(s_one);
System.out.println(alignment.toString());
System.out.println(s_two);