Problem: DNA-3, Finding Proteins

Problem Statement

Your method should find the first protein (if there is one) and return the number of base-pairs in the protein. If the digital representation of the DNA is good, this number will be a multiple of three since there are three base-pairs per codon.

If there is no protein in the DNA, return -1.

Definition

• Class: ProteinFinder
• Method: length
• Parameters: String
• Returns: int
• Method signature:

    int length(String dna)
  

  (be sure your method is public)

  Class

  public class ProteinFinder { public int length(String dna) { // fill in code here } };

  Notes

  You'll want to use both String methods indexOf, one that takes a single parameter and one that has a String and an int parameter that specifies where the search will start. See javadoc for java.lang.String which is part of Javadoc for all all classes

  Constraints

  • The String dna contains only the characters 'A', 'G', 'T', 'C' (uppercase).

  • The String dna is between 0 and 1000 characters long (inclusive).

  Examples

  1.    CGATGCATCCCTTTACTTAACCAG
     
     

     Returns: 12, here is the DNA exploded to show the protein between the start and stop codons.

        CG ATG CATCCCTTTACT TAA CCAG
           ^^^              ^^^
          start            stop
     

  2.   CCCCATGAAATTTCCCGGG
     
     

     Returns: -1, there is a start codon, but no stop codon.

  3.   CCCCTAACCCATGAAATTTCCCGGG
     
     

     Returns: -1, there is a start codon, but no stop codon after the start codon --- note that there is a stop codon before the start codon, but this strand doesn't code for a protein.

  4.   ATGTGA
     
     

     Returns 0, there is no protein, but there are start and stop codons.

  ---

  Owen L. Astrachan
  Last modified: Mon Sep 19 20:56:19 EDT 2005