/**
 * This class represents a DNA sequence of nucleotides 'A', 'T', 'C' and 'G' as
 * a sequence of characters in a {@link String} object.
 * 
 * @author iCarnegie
 * @version 1.0.0
 */
public class DNASequence {

	/**
	 * Test driver for class <code>DNA</code>.
	 * 
	 * @param args
	 *            not used.
	 */
	public static void main(String[] args) {

		String s = "ATTATCGGGGTAA";
		DNASequence dnaSequence = new DNASequence(s);

		if ((dnaSequence.getNumberOfA() == 4)
				&& (dnaSequence.getNumberOfT() == 4)
				&& (dnaSequence.getNumberOfC() == 1)
				&& (dnaSequence.getNumberOfG() == 4)) {
			System.out.println("Test case 1:  get methods passed\n");
		} else {
			System.out.println("Test case 1:  get methods failed !!!\n");
		}

		if (dnaSequence.twoConsecutive('T')) {
			System.out.println("Test case 2: method twoConsecutive passed\n");
		} else {
			System.out
					.println("Test case 2: method twoConsecutive failed !!!\n");
		}

		if (dnaSequence.twoConsecutive('A')) {
			System.out.println("Test case 3: method twoConsecutive passed\n");
		} else {
			System.out
					.println("Test case 3: method twoConsecutive failed !!!\n");
		}

		if (!dnaSequence.twoConsecutive('C')) {
			System.out.println("Test case 4: method twoConsecutive passed\n");
		} else {
			System.out
					.println("Test case 4: method twoConsecutive failed !!!\n");
		}

	}

	/* Contains the sequence of nucleotides. */
	private String sequence;

	/* Contains the number of nucleotide A */
	private int numberOfA;

	/* Contains the number of nucleotide T */
	private int numberOfT;

	/* Contains the number of nucleotide C */
	private int numberOfC;

	/* Contains the number of nucleotide G */
	private int numberOfG;

	/**
	 * Constructs a <code>DNASequence</code> object that represents the
	 * sequence of nucleotides indicated by the chars in the <code>string</code>
	 * argument and counts the occurrences of each nucleotide in the sequence.
	 * 
	 * @param initialSequence
	 *            a string with the initial sequence of nucleotides.
	 */
	public DNASequence(String initialSequence) {

		sequence = initialSequence;
		countNucleotides();
	}

	/*
	 * Counts the occurrences of each nucleotide in the DNA sequence and then
	 * updates the values of the variables numberOfA, numberOfT, numberOfC, and
	 * numberOfG .
	 */
	private void countNucleotides() {

		// delete "int"
		numberOfA = 0;
		numberOfT = 0;
		numberOfC = 0;
		numberOfG = 0;

		int index = 0;

		while (index < sequence.length()) {

			char nucleotide = sequence.charAt(index);

			if (nucleotide == 'A') {
				numberOfA++;
			} else if (nucleotide == 'T') {
				numberOfT++;
			} else if (nucleotide == 'C') {
				numberOfC++;
			} else if (nucleotide == 'G') {
				numberOfG++; // "numberOfC++"->"numberOfG++"
			}
			index++;
		}

		return;
	}

	/**
	 * Obtains the number of occurrences of nucleotide A in the sequence.
	 * 
	 * @return the number of occurrences of nucleotide A.
	 */
	public int getNumberOfA() {

		return numberOfA;
	}

	/**
	 * Obtains the number of occurrences of nucleotide C in the sequence.
	 * 
	 * @return the number of occurrences of nucleotide C.
	 */
	public int getNumberOfC() {

		return numberOfC;
	}

	/**
	 * Obtains the number of occurrences of nucleotide G in the sequence.
	 * 
	 * @return the number of occurrences of nucleotide G.
	 */
	public int getNumberOfG() {

		return numberOfG;
	}

	/**
	 * Obtains the number of occurrences of nucleotide T in the sequence.
	 * 
	 * @return the number of occurrences of nucleotide T.
	 */
	public int getNumberOfT() {

		return numberOfT;
	}

	/**
	 * Checks if the nucleotide specified by the argument occurs in two
	 * consecutive locations in the DNA sequence.
	 * 
	 * @param input
	 *            a <code>char</code> that represent the nucleotide.
	 * @return <code>true</code> if the specified nucleotide occurs two
	 *         consecutive locations in the sequence. Returns <code>false</code>
	 *         otherwise.
	 */
	public boolean twoConsecutive(char input) {

		int index = 1;

		// "sequence.length()-1"->"sequence.length()"

		while (index < sequence.length()) {

			int indexOfFirstNucleotide = index - 1;

			char firstNucleotide = sequence.charAt(indexOfFirstNucleotide);
			char secondNucleotide = sequence.charAt(index);

			// "||"->"&&"

			if ((firstNucleotide == input) && (secondNucleotide == input)) {

				return true;

			}
			index++;
		}

		return false;
	}

}