Question

Help on a java programming problem

Given two sequences, where one is a substring of the other, we define a substring alignment by matching the substring with the longer sequence and placing gaps everywhere else. For example if the input is ACCTGTAGG and TGT then the substring alignment is
ACCTGTAGG
---TGT---

i need help designing program that prints the substring alignment of two unaligned sequences. If no substring alignment exists then the program should print "No alignment found"...im puzzled over this situation

Any advice on how to start?

Thank in advance

Answer 1

Here is the completed code for this problem. Comments are included, go through it, learn how things work and let me know if you have any doubts or if you need anything to change. If you are satisfied with the solution, please rate the answer. Thanks

// SubstringAlignment.java

import java.util.Scanner;

public class SubstringAlignment {

      // method to find substring alignment of two strings and print it

      public static void printSubstringAlignment(String s1, String s2) {

            // checking if s1 is not a substring of s2 and s2 is not a substring of

            // s1

            if (!s1.contains(s2) && !s2.contains(s1)) {

                  // no alignment

                  System.out.println("No alignment found");

            } else {

                  char align[];

                  // checking if s1 contains s2 (s1 will be the bigger string)

                  if (s1.contains(s2)) {

                        // finding index of occurrance of s2 in s1

                        int index = s1.indexOf(s2);

                        // converting s1 into a char array

                        align = s1.toCharArray();

                        // filling all elements before index in align array with '-'

                        for (int i = 0; i < index; i++) {

                              align[i] = '-';

                        }

                        // filling all elements after index+s2.length in align array

                        // with '-'

                        for (int i = index + s2.length(); i < align.length; i++) {

                              align[i] = '-';

                        }

                        // displaying s1

                        System.out.println(s1);

                        // displaying alignment after converting align to String

                        System.out.println(new String(align));

                  } else {

                        // doing the same with s1 and s2 swapped.

                        int index = s2.indexOf(s1);

                        align = s2.toCharArray();

                        for (int i = 0; i < index; i++) {

                              align[i] = '-';

                        }

                        for (int i = index + s1.length(); i < align.length; i++) {

                              align[i] = '-';

                        }

                        System.out.println(s2);

                        System.out.println(new String(align));

                  }

            }

      }

      public static void main(String[] args) {

            Scanner scanner = new Scanner(System.in);

           

            //asking and reading two strings

           

            System.out.print("Enter first String: ");

            String s1 = scanner.nextLine();

            System.out.print("Enter second String: ");

            String s2 = scanner.nextLine();

           

            //printing substring alignment if exists

            printSubstringAlignment(s1, s2);

      }

}

/*OUTPUT (multiple runs)*/

Enter first String: ACCTGTAGG

Enter second String: TGT

ACCTGTAGG

---TGT---

Enter first String: java programming is fun

Enter second String: is

java programming is fun

-----------------is----

Enter first String: very cool

Enter second String: this is a very cool phone

this is a very cool phone

----------very cool------

Enter first String: some text

Enter second String: some other text

No alignment found