CompactGenome.java

Below is the syntax highlighted version of CompactGenome.java from §3.3 Designing Data Types.

/******************************************************************************
 *  Compilation:  javac CompactGenome.java
 *  Execution:    java CompactGenome
 *
 *  CHANGE TO USE CHAR ARRAY, AND PACK 8 TO THE CHAR
 *  BOOLEAN ARRAY IN JAVA USES 4 BITS PER VALUE (INSTEAD OF ONE)
 *
 ******************************************************************************/

public class CompactGenome {
    private boolean[] a = new boolean[2];
    private int N = 0;


    // double the size of the array
    private void resize() {
        boolean[] temp = new boolean[2*a.length];
        for (int i = 0; i < a.length; i++)
            temp[i] = a[i];
        a = temp;
    }

    public void addNucleotide(char c) {
        if (2*N == a.length) resize();
        if (c == 'A')  {
            a[2*N] = false;
            a[2*N + 1] = false;
        }
        else if (c == 'C') {
            a[2*N] = false;
            a[2*N + 1] = true;
        }
        else if (c == 'G') {
            a[2*N] = true;
            a[2*N + 1] = false;
        }
        else if (c == 'T') {
            a[2*N] = true;
            a[2*N + 1] = true;
        }
        else throw new RuntimeException("Illegal nucleotide");
        N++;
    }


    public char nucleotideAt(int i) {
        if (i >= N || i < 0) throw new RuntimeException("Genome out of bounds");
        if      (a[2*i] == false && a[2*i + 1] == false) return 'a';
        else if (a[2*i] == false && a[2*i + 1] == true)  return 'c';
        else if (a[2*i] == true  && a[2*i + 1] == false) return 'g';
        else                                             return 't';
    }

    public int length() { return N; }



    // sample client for testing
    public static void main(String[] args) {
        CompactGenome genome = new CompactGenome();
        genome.addNucleotide('A');
        genome.addNucleotide('G');
        genome.addNucleotide('C');
        genome.addNucleotide('C');
        genome.addNucleotide('T');
        for (int i = 0; i < genome.length(); i++) {
            StdOut.print(genome.nucleotideAt(i));
        }
        StdOut.println();


    }

}