Class DNA

java.lang.Object

DNA

public class DNA
extends java.lang.Object

A class that represents a DNA sequence.

Internally the class represents DNA as a string. You are responsible for implementing the longest common subsequence method and a straightforward constructor.

The DNA class does not need to provide a setter for the sequence, meaning that it can be allowed to not change after the instance is created. As a result, it should not provide an empty constructor.

See Also:

MP5 Documentation

Constructor Summary

Constructors

Constructor	Description
DNA(java.lang.String setSequence)	Create a new DNA instance from the given sequence of base pairs.

Method Summary

Modifier and Type	Method	Description
static DNA	getLongestCommonSubsequence(DNA firstSequence, DNA secondSequence)	Return the longest common subsequence of the two provided DNA sequences.
java.lang.String	getSequence()	Gets the sequence of base pairs for this DNA instance.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

DNA

public DNA(java.lang.String setSequence)

Create a new DNA instance from the given sequence of base pairs.

The constructor should validate and normalize its inputs. All characters in the string should be from the set A, T, C, and G (this in DNA, not RNA). You should accept lower-case inputs but convert them to upper-case for the purposes of later comparison.

Parameters:

setSequence - the sequence of base pairs to initialize the instance with

Method Detail

getSequence

public java.lang.String getSequence()

Gets the sequence of base pairs for this DNA instance.

Returns:

the sequence of base pairs for this DNA instance

getLongestCommonSubsequence

public static DNA getLongestCommonSubsequence(DNA firstSequence,
                                              DNA secondSequence)

Return the longest common subsequence of the two provided DNA sequences.

You should complete a recursive implementation of this algorithm. You may want to use a helper function so that you can recurse on strings, which have helpful methods, rather than the DNA sequence object.

A recursive solution to this problem can get quite slow, particularly as the length of the sequences to compare increases. The testing timeouts provided should be sufficient and will be adjusted as needed. However, feel free to investigate and consider faster approaches.

Parameters:

firstSequence - the first DNA sequence to compare

secondSequence - the second DNA sequence to compare

Returns:

the longest common subsequence between the two provided DNA sequences

See Also:

Longest Common Subsequence