/**
* This class represents a DNA sequence of nucleotides 'A', 'T', 'C' and 'G'
* as a sequence of characters in a {@link String} object.
*
* @author vivizhyy
* @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("numberA = "+dnaSequence.getNumberOfA());
//System.out.println("numberT = "+dnaSequence.getNumberOfT());
//System.out.println("numberC = "+dnaSequence.getNumberOfC());
//System.out.println("numberG = "+dnaSequence.getNumberOfG());
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;
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++;
}
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)) {
if ((firstNucleotide == input) && (secondNucleotide == input)) {
return true;
}
index++;
}
return false;
}
}
==============================================================================================
Results:
Test case 1: get methods failed !!!
Test case 2: method twoConsecutive passed
Test case 3: method twoConsecutive passed !!!
---------------------------------------------------------------------------
Bug #1
Description of the bug:
When the index gets 13, and the numberOfC = 5,numberOfG = 0 ;
Lines of source code that contain the bug:
103:} else if (nucleotide == 'G') {
104: numberOfC++;
Lines of the fixed code:
103:} else if (nucleotide == 'G') {
104: numberOfG++;
---------------------------------------------------------------------------
Bug #2
Description of the bug:
the numberOfA=0,numberOfT=0,numberOfG=0,numberOfC=0
Lines of source code that contain the bug:
private void countNucleotides() {
int numberOfA = 0;
int numberOfT = 0;
int numberOfC = 0;
int numberOfG = 0;
Lines of the fixed code:
private void countNucleotides() {
//int numberOfA = 0;
//int numberOfT = 0;
//int numberOfC = 0;
//int numberOfG = 0;
---------------------------------------------------------------------------
Bug #3
Description of the bug:
the function twoConsecutive(char input) is used to couunt the number of
A,G,C,T is two or not.
Lines of source code that contain the bug:
if ((firstNucleotide == input) || (secondNucleotide == input)) {
Lines of the fixed code:
if ((firstNucleotide == input) && (secondNucleotide == input)) {
---------------------------------------------------------------------------
Bug #4
Description of the bug:
the loop while(index < sequence.length() - 1)
dosen't count the last A
Lines of source code that contain the bug:
while (index < sequence.length() - 1) {
Lines of the fixed code:
while (index < sequence.length()) {
---------------------------------------------------------------------------