ssd3：Practical Quiz 2 Debugging Class DNASequence

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

 /* 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;

 /**
  * 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");
  }
 }

 /**
  * 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()  {

 /* int numberOfA = 0;
  int numberOfT = 0;
  int numberOfC = 0;
  int numberOfG = 0;   */
  
  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') {
    numberOfC++;
   } */
   else if (nucleotide == 'G') {
    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 T in the sequence.
  *
  * @return  the number of occurrences of nucleotide T.
  */
 public int  getNumberOfT( )  {

  return numberOfT;
 }

 /**
  * 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;
 }

 /**
  * 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;

 /* while (index < sequence.length() - 1) {  */
  
  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;

   }  */
   
   if ((firstNucleotide == input) && (secondNucleotide == input)) {

    return true;

   } 
   
   index++;
  }

  return false;
 }
}

 

 

 

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