COSC 2P03 Advanced Data Structures: Assignment 3. Define a method named loadData in the DrugDesign class.

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COSC 2P03 Advanced Data Structures: Assignment 3

 

1Department of Computer Science, Brock University

 

1 Introduction to the Problem

A drug is a small molecule that can bind to a target to inhibit or activate a pathway. However, not every

compound can be used a medicine. To select drug candidates, a few physicochemical properties need to be

first considered. In this assignment, you need to use the three sort algorithms - heap sort, quick sort, and

merge sort, to sort molecules based on given properties.

2 Your Tasks (12 Marks)

1. Define a class named DrugDesign which should include data attributes named originalData and

finalSortedData, and the following methods. Feel free to define other variable and method attributes

in the class.

2. Define a method named loadData in the DrugDesign class. This method should take a filename

(of course with absolute or relative path) as the input parameter and store the loaded data in the

originalData variable. (A CSV file named ZINCSubset.csv is provided. You should load this file

using method loadData in the main function). The originalData variable is an array with each

element stores a row in the text file. Thus, each element of your array should be an object of a data

item class with the following variables: smiles (string), fragments (string), n fragments (integer),C

(integer), F (integer), N (integer), O (integer), Other (integer), SINGLE (integer), DOUBLE (integer),

TRIPLE (integer), Tri (integer), Quad (integer), Pent (integer), Hex (integer), logP (float), mr (float),

qed (float), and SAS (float) where corresponding data types are indicated in brackets. (2 marks)

3. Define a method named heapSort in the DrugDesign class to implement the max-heap based heap

sort algorithm (in incremental order). This method should take a 1-D array as input, and finally

return the sorted indices only as an array of integers. For example if you have an array with values

[3.1,5.2,2.3,1.4,6.5], the method should return [ 3, 2, 0, 1, 4 ]. (2 marks)

4. Define a method named quickSort in the DrugDesign class to implement the quick-sort algorithm (in

incremental order) discussed in our lectures. Similar to the above method, quickSort should take a

1-D array as input, and only return the sorted indices. (2 marks)

5. Define a method named mergeSort in the DrugDesign class to implement the merge sort algorithm (in

incremental order) learned from this course. Similar to the above two methods, mergeSort should take

a 1-D array as input, and only return the sorted indices. (2 marks)

6. Define a method named sumRankSort in the DrugDesign class. This method should take the three 1-D

arrays of indices as input, take element-wise sum and store it in a local 1-D array named sumOfRanks,

and then sort sumOfRanks using a method of your choice (heapSort, quickSort, or mergeSort), and

finally return the sorted indices. (1 mark)

7. In the main function, you should following the following steps:

∗E-mail address: yli2@brocku.ca yifeng.li.cn@gmail.com

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(a) Create an instance of the DrugDesign class. (0.25 mark)

(b) Call the loadData method to read data from ZINCSubset.csv to variable originalData. (0.25

mark)

(c) Call the heapSort method to sort the original data based on property logP. Note that you should

not really change originalData. Just obtain the sorted indices. (0.25 mark)

(d) Call the quickSort method to sort the original data based on property mr. Note that you should

not really change originalData. Just obtain the sorted indices. (0.25 mark)

(e) Call the mergeSort method to sort the original data based on property SAS. Note that you should

not really change originalData. Just obtain the sorted indices. (0.25 mark)

(f) Call the sumRankSort method to take the results of the above three function calls as input and

obtain the sorted indices. (0.25 mark)

(g) Based on the result of the previous step, sort our original data, store it in variable finalSortedData

(this variable should have the same format as originalData), and save the information from

finalSortedData to a CSV file named ZINCSubset sorted.csv. (0.5 mark)

Program comments: to maximize readability, you should properly comment your program. (1 mark)

3 Submission

• Your source code.

• A PDF printout of your source code.

• The text file ZINCSubset sorted.csv that shows all expected outputs from these tasks.

• Compress the above files in a zipped folder named COSC2P03 A2 YourFirstname YourLastname StudentNumber.zip

and submit it through Sakai before indicated due time.

• Late submissions will not be accepted.

• Note: you should submit both your Java source code and your PDF printout. Missing any of them will

result in a zero grade for this assignment.

4 Academic Integrity

This assignment should be tackled individually. Outsourcing or teamwork is not allowed. Violation of this

requirements will be seriously processed in accordance with university policies.

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