ssd3：Practical Quiz 2 Debugging Class DNASequence

原创于 2011-02-07 10:51:00 发布 · 1.9k 阅读

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#class #debugging #string #input #methods #variables

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本文介绍了一个用于分析DNA序列的Java类，该类可以统计序列中四种核苷酸的数量，并检查特定核苷酸是否连续出现两次。

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/**
* 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;
}
}

考察：

对程序进行调试。