Question

Java help
able to create a method that return. it checks for malformed genome and sequence

The user inputs a genome that is represented as a string composed of letters A,C,G and T of any length. Also user enter a sequence that is also represented as a string composed of letters A,C,G and T of any length.

Example
Not a malformed genome
CATGCAATGCATA
ATACGTAACGTAC

not a malformed sequence
GCATA
ATACG

Example
malformed genome
CATGCICATA ----> because of the I the genome is malformed and the genome contains characters other than A,C,G and T.

malformed sequence
CIIA ----> because of the I the sequence is malformed and the sequence contains characters other than A,C,G and T.

any advice
thanks in advance

Answer 1

CODE:

import java.util.Scanner;
public class MalformedGenome {

   //method to determine a genome sequence is bad or not
   public static boolean determineMalformedGenome(String sequence) {
       //converting the string sequrnce to character array
       char[] seqArray = sequence.toCharArray();
       //boolean variable badGenome
       boolean badGenome = false;
       //checking the genome sequence
       //character-wise to determine
       //it is bad or not
       for (int i = 0; i < seqArray.length; i++) {
           //if the genome contains any of the
           //characters other than ACGT
           // it is a bad genome, else not
           if(seqArray[i] == 'A' || seqArray[i] == 'C' || seqArray[i] == 'G' || seqArray[i] == 'T') {
               badGenome = false;
           }
           else {
               badGenome = true;
               break;
           }
       }
       //returning the badGenome
       return badGenome;
   }
   //driver code
   public static void main(String[] args) {
       //instantiating the Scanner class
       Scanner input = new Scanner(System.in);
       //prompt to enter the genome sequence
       System.out.print("Enter a sequence of genome: ");
       //getting the input sequence
       String sequence = input.nextLine();
       //calling the method to determine the malformed genome
       if(determineMalformedGenome(sequence)){
           System.out.println("This is a malformed genome");
       }else{
           System.out.println("This is not a malformed genome");
       }
   }  
}

OUTPUT: