辅导CSE 11程序、写作Java课程编程

” 辅导CSE 11程序、写作Java课程编程CSE 11 Winter 2021 PA2 – COVID GenomicSequenceDue date: Tuesday, Jan 19 @ 11:59PM PST(Wednesday, Jan 20 @ 11:59PM PST w/ slip day. If you submit your assignment late, the autograder willautomatically use your slip day if you have any remaining. Note that the README portion of this assignmentcannot be submitted late.)Provided FilesNone.Files to SubmitCovidGenomeAnalysis.javaCovidMutation.javaGoal:Programming Assignment 2 is an introduction to loops and Strings in Java. You will use loops, String methods,and other programming techniques to complete the assignment.Please read the entire write-up before getting started.Some General NotesMost of these notes are necessary for autograding purposes. If any of these does not make sense, youprobably arent doing anything that it applies to. However, you should make sure that when you do learnabout it later on in this quarter that you follow these notes. We cannot be lenient regarding these thingsbecause everything is autograded to ensure fairness.Make sure to read the autograder output after you submit to Gradescope (wait until the autograder isfinished running).Match the specifications that we provide exactly, otherwise we cannot ensure that the autograder willfunction correctly. This includes file names, class names, method signatures, extending, throwing, etc.Constants should be defined as private static final variables.Do not use any static variables (other than for constants) or instance variables that are not specified in thiswriteup. We cannot ensure that these do not get clobbered during grading. Any extra variables used shouldbe local only.Unless otherwise Specified, do not add any extra import s or use any packages not from java.lang otherthan those implied or explicitly named by this writeup.Do not specify a package for your files. This will cause them to fail to compile with the autograder.Do not add any extra Classes to your files and do not write code in files that are not specified.Do not call helper methods except from the class where they are implemented, as we will be using our ownversion of classes during grading (which will only have the instance variables and methods specified in thiswriteup). You shouldnt be able to call them anyway if you have declared them as private .If a behavior (say, on some specific input) is not specified, you may handle that case however you want.However, if you implement a specific behavior for some special case of a required method, do not rely onthat specific behavior when using that method as a helper method (only assume that the method works asspecified in the writeup).For the surveys and AI form, make sure you are filling them out and specifying your email address as theone linked with your Gradescope account. If you fill them out after submitting, you can either resubmit toupdate your score immediately or wait for us to rerun the autograder for everyone after the deadline.Any late submission will trigger a slip day usage for this assignment. There will be no exceptions foraccidents, since we cannot determine if it is an actual accident. If you need special accommodations,please email the Professor directly.Part 1: CovidGenomeAnalysis.javaYou have just been recruited to join a lab working on the genetic sequence of COVID-19 because of the skillsyou demonstrated in the first PA of CSE 11. You will now use your knowledge of computer science to helpscientists develop a more effective and cheaper vaccine for COVID-19.COVID-19 is a RNA virus, meaning that its genetic sequence is made of adenine (A), cytosine (C), guanine (G),and uracil (U). This is in contrast with DNA, which has thymine (T) instead of uracil. However, because ofinstability of RNA, it must be converted into DNA to be sequenced (you can read more about this here). For thisreason, we will use the complementary DNA for this assignment. In other words, the genome we are using willcontain A, T, C, and G.A DNA molecule consists of two strands wound around each other, with each strand held together bybonds between the nitrogenous nucleobases. Adenine (A) pairs with thymine (T) and cytosine (C) pairswith guanine (G).Reference: httpss://www.genome.gov/genetics-glossary/acgtTaskWe want to first run some simple analyses. Given what we know about DNA, if we know the bases on one strandof the DNA, we can know which Bases are on the other strand of the DNA. We also want to count the number oftimes a specific base appears on one strand. We will implement this in the main() method of theCovidGenomeAnalysis class in the CovidGenomeAnalysis.java file.public class CovidGenomeAnalysis {…}public class CovidGenomeAnalysis {…public static void main(String[] args);…}InputJust like in PA1, we will read user input from System.in using a Scanner (remember to import it). After a userruns java CovidGenomeAnalysis , they will then type the input to our program. For this assignment, you cansafely assume that this input will come as a single line of characters and that each character before the newlinecharacter is a capital letter A, T, C, or G.OutputAfter reading in the string given as input, we will print some output to System.out . This printout will always betwo items, separated by a single space, followed by a single newline character. The System.out.println() methodwill print whatever String is passed in followed by a newline, so if you use it, you do not need to explicitly add anewline character. If you use System.out.print() , you will need to add the newline character yourself. There is noinvalid input case (as we are assuming the input will always follow the format above), so the first item should bethe number of thymine (T) nucleotides that appear in the strand opposite the input sequence and the second itemshould be the strand opposite the input sequence. The opposite strands bases should be in the order determinedby the input strand and should only contain the capital characters A, T, C, and G.ImplementationValid InputsYour program should work for any input that does not have characters other than A, T, C, and G.TestingIt would be easier to use input from a file rather than typing the input each time we want to test our code. Wehavent learned file IO yet, but we can still do it with the Scanner from System.in and pipe input to System.infrom a file.There are many ways to do this, but the following way is pretty system agnostic. First, we will need to makesome file whose raw data has the genome sequence we want to use as input (as the first line). For this purpose,we should use the .txt extension for the file name to avoid confusion. To have the .txt file be read fromSystem.in , we will use a Combination of the cat command and | (pipe) symbol.Cat is short for concatenate. If wWe were to just do cat file.txt , it would display the content of the file.txt to theterminal. We instead then use | to redirect the output of a command to the input of another. In our case, we willbe redirecting the output of the cat command into the input of our Java program.(For Windows users, cat is available in PowerShell. If you are using command prompt, the equivalent commandis type .)Sample Test CaseCase 1Input: ACGTAAGCAOutput: 4 TGCATTCGT (there are 4 letter T s in the output sequence)You can run this case by having a file sample1.txt with the contents:and running the command cat sample1.txt | java CovidGenomeAnalysis .ACGTAAGCAPart 2: CovidMutation.javaYou are recruited to another research lab at UCSD because of your exceptional work in helping create a newvaccine. This lab is on the forefront of a COVID-19 cure using an antibody treatment. This antibody treatmentworks by mutilating the genome sequence of the COVID-19 virus such that the nucleotides formed by thismutilated sequence turn the virus into a clump of molecules that is easily broken down by white blood cells. Theresearch lab has a genome sequence simulator that takes in a string of nucleobases (Adenine, Guanine, Thymine,Cytosine, Uracil) and simulates the DNA/RNA chain of that potential organism and its characteristics. The labhas found that they Can control the antibodies to specifically reverse every k (some integer) nucleobases of thevirus. In order to produce this treatment with the greatest efficacy possible, the research lab must find some k thathas the highest rate of weakening the COVID-19 virus.TaskGiven some genome sequence, we want to find the output if we did this k-reversing. Since this technique mightbe used in the future, we will allow it to work for any string and hope the researchers pass in a valid genomesequence for now. Our application should be able to take any string and any integer k and reverse every k-sizedchunk of the string. We will implement this in the main() method of the CovidMutation class in theCovidMutation.java file.InputWe will read user input from System.in using a Scanner (remember to import it). After a user runs javaCovidMutation , they will then Type the input to our program. For this assignment, you can safely assume that thisinput will come as a single line of characters followed by an integer on the next line. The first line will be thestring to k-reverse (all you need to know is that it is a string of characters) and the integer k in the next line willrepresent the chunk size.OutputAfter checking the inputs, we will Print some output to System.out . This printout will always be a single stringfollowed by a single newline character. In the case of invalid inputs (see below), print out the original input string(the string from the first line of input). In the case of valid inputs, print out the k-reversed version of the inputstring. If the length of the string is not divisible by k then you should reverse all characters in the remainder of thestring after the last full chunk. If the given k is greater than the length of string, you should completely reversethe entire string (this is a special case of the case described in the previous sentence). Note that this means thatthe output should Always have the same length as the input string.public class CovidMutation {…}public class CovidMutation {…public static void main(String[] args);…}ImplementationValid InputsThe first line will be any string (i.e., possibly composed of characters other than A, C, T, and G). The integer inthe second line must be at least 1 to be valid.TestingYou can use the same procedure as for Part 1. The only difference will be that the second line of your input filewill contain the integer representing the chunk size.Sample Test CaseCase 1Input: sequence = ACGTAAGCA ; k = 3Output: GCAAATACG (the k chunk size given is 3 which means we will reverse every 3nucleotides. This gives ACG|TAA|GCA, if we are to reverse each chunk we will haveGCA|AAT|ACG.)Case 2Input: sequence = ACGTAAGCA ; k = 7Output: GAATGCAAC (the k chunk size given is 7 which means we will reverse every 7nucleotides. This gives ACGTAAG|CA, if we are to reverse the first full chunk we will haveGAATGCA. If there is a remainder left that is smaller than the k given, it should be fully reversed. Inthis case we have 2 nucleobases (CA) left and those should be reversed to result in GAATGCA|AC.)StyleCoding style is an important part of ensuring readability and maintainability of your code. We will grade yourcode style in all submitted code files according to the style guidelines. Namely, there are a few things you musthave in each file/class/method:1. File headers2. Class headers3. Method headers4. Inline comments5. Proper indentation (do not intermingle spaces and tabs for indentation)6. Descriptive variable names7. No magic numbers8. Reasonably short methods (if you have implemented each method according to specification in this writeup,youre fine)9. Lines shorter than 80 characters (note, tabs will be counted as 4 characters toward this limit. It is a goodidea to set your tab width/size to be 4. A good way to check is using the command grep -n .\{81,\} *.javain the directory with your files, but note that this wont necessarily take tabulation into accountappropriately.)10. Javadoc conventions (@param, @return tags, /** header comments */, etc.)A full style guide can be found here. In addition, an example of a properly styled Java file can be found here. Ifyou need any clarifications, feel free to ask on Piazza.READMEAll the questions for the README Portion of this assignment can be found on Gradescope. Note that this portionof the assignment cannot be submitted late.SurveyPlease fill out this survey, worth 1 point to your PA grade, to help us improve the experience of this class! We askthat you write thoughtful and truthful answers, to the best of your ability. Your specific answers will not affectyour grade in any way. You will receive credit as long as you complete it.Weekly Reflection 2.Submission:Turning in your codeSubmit all of the Following files to Gradescope by Tuesday, Jan 19 @ 11:59PM PST (Wednesday, Jan 20 @11:59PM PST w/ slip day):CovidGenomeAnalysis.javaCovidMutation.javaWhen submitting, please wait until the autograder finishes running and read the output. Your code must compilein the autograder in order to receive proper partial credit. Make sure that you have followed the GeneralNotes to ensure that the autograder can run.Evaluation1. Correctness (89 points)You will earn points based on the autograder tests that your code passes. If the autograder tests are not ableto run (e.g., your code does Not compile or it does not match the specifications in this writeup), you maynot earn credit.2. Coding Style (5 points)3. README (5 points)4. Weekly Reflection Survey (1 point)如有需要，请加QQ：99515681 或WX：codehelp

“