Java，Array。
Objectives
Upon completion of this assignment, you need to be able to:
- Iterate through an array from its beginning index to the end.
- Determine cumulative information as you progress through an array.
- Determine equality of string objects.
- Access the individual characters of a string object in Java.
- Continue building good programming skills.
Introduction
An important task in bioinformatics is the identification of DNA and RNA sequences. In this assignment, we will be looking at nucleic acid sequences. These sequences contain up to four different bases denoted by letters: A for adenine, C for cytosine, G for guanine, and T for thymine. Sequence strings are compared in order to determine whether nucleic acid sequences match each other, or are related through mutations. Real sequence data, as used by biochemists and in bioinformatics research, consists of very long strings of bases. Determining relatedness can require the use of very complex algorithms, beyond the scope of this assignment.
The sequences in this assignment will all contain between two and four of the possible bases in {A, C, G, T}. Your task to to search through a collection of sequence data and count how many times a specific sequence occurs. For example, if the collection contains the following sequences: {ACTG, GATC, ACT, GTC, AC, GATC, GA} and we search for the specific sequence GATC, we would report that it was found 2 times.
One of the challenges in this assignment will be dealing with mutated sequences. A mutation can occur due to insertions of additional bases within a sequence. For the purpose of this assignment, a mutated sequence contains at least two of the same bases occurring in a row; for example, in the sequence GAAATC, the A has mutated, and in the sequence CCGGAT, both the C and G have mutated. Another task in this assignment is to detect how many of the sequences in the collection are mutated. The final task will be to search through the collection of sequence data for a specific sequence, but you must treat original and mutated sequences the same. For example, if the collection contains {TGC, AC, TTGC, TACG, TGGCC, AGTC} and we search for the specific sequence TGC, we would report that it was found 3 times, because TTGC and TGGCC are mutated forms of TGC.
Quick Start
(1) Download this pdf file and store it on your computer.
(2) Create a directory / folder on your computer specific to this assignment. for example, CSC110/assn5 is a good name.
(3) Save a file called DNASequencing.java in your directory. Fill the source code with the class name and the methods outlined in the following specification document. Make sure the method headers are exact copies.
(4) Start with the easiest methods first. See the following detailed instructions below for some tips.
(5) Complete each method and test it thoroughly before moving onto the next one. Compile and run the program frequently; it is much easier to debug an error shortly after a successful and error-free run.
Detailed Instructions
We offer the following organization of the parts of the programming task. For more details about what each of the method does, check out the specification document. This document has several links to the Java String class. Look through the method summary for methods that let you manipulate string objects. You already know about the length method. You may find the toCharArray helpful as well.
In the following subsections, we provide a detailed description of how to approach the implementation of each of the methods named in the DNASequencing class:
Start with printArray
This is a good warmup exercise. Use a for loop to visit each element in the array input parameter. Remember that array indices start at 0, as do the indices of each character in a String.
findLongest and findFrequency
After completing and testing printArray, work on the findLongest or the findFrequency methods; they are similar. Within both methods, use a loop to visit each element in the array. In the findLongest method, you must keep track of which String object in the array contains the most characters, whereas in the findFrequency method, you must keep track of how many times a specific String object is found in the array. Make sure you finish and test both of these before moving to the next step.
The methods that involve mutations
These methods deal specifically with the DNA sequences, so you can assume that the input parameters are legitimate DNA sequences, even though they are of type String.
hasMutation
This method is probably the easier one to implement, so you can start with that. For those of you who like an extra challenge, consider writing a more general method that deals with any string and returns true if there are consecutive characters that are identical. Experienced programmers often look for ways to make code that is re-usable, easy to maintain, and modular. For example, suppose that you wish to create a more general method (for possible future use) that deals with any string. And suppose it is called hasCharacterRun.
After fully testing it, it is stored in your personal library (or toolkit) of code. Now, the hasMutation method is very simple and requires no testing:
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* Determines if a DNA sequence is mutated, i.e. has repeated characters.
* input: sequence A String sequence of two to four
* of the following characters: #123;A,C,G,T#125;
* returns: true if the DNA sequence is mutated, false if it is not.
*/
public static boolean hasMutation(String sequence) #123;
return hasCharacterRun(sequence);
#125;
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countTotalMutations
Implement this method by building on the technique for findFrequency and adding calls to hasMutation.
findFreqWithMutations
This method examines the contents of the sequence array, looking for a specific sequence and its mutations. By the time you have done all the other methods, this should be reasonably simple. You may want to create a helper method, but it is not required.
Building and testing
As you work through a solution, we strongly recommend that you save, compile and test the code after every line or two. This can be something as easy as printing out the value of a variable, or calling a method to print out the value returned. It is important to do this to confirm a component of the code works correctly, so you can be confident using that component throughout the code in later steps.
For each of the methods listed in the specifications, you must provide an internal test call from the main method If the method does not behave as expected, then debug and adjust the method. To receive full marks for testing, each method must be tested, even if it does not work.
Examples
We provide a couple of internal test cases you can use to test the correctness of the methods. The following diagrams demonstrate some sample testing for the printArray and findLongest methods.
Submission
Submit the following completed file to the Assignment folder on conneX.
- DNASequencing.java
Please make sure you have submitted the required file(s) and conneX has sent you a confirmation email. Do not send [.class] (the byte code) files. Also, make sure you submit your assignment, not just save a draft. Draft copies are not made available to the instructors, so they are not collected with the other submissions. We can find your draft submission, but only if we know that it’s there.
A note about academic integrity
It is OK to talk about your assignment with your classmates, and you are encouraged to design solutions together, but each student must implement their own solution.
Grading
Marks are allocated for . . .
- No errors during compilation of the source code.
- The method headers must be exactly as specified and the methods must perform as specified. Be sure to read the Method Details in the specification document.
- Each method must have a test call inside the main method.
- Style of the source code meets the requirements outlined in the Coding conventions document available in the Lab Resources folder of conneX.