INF 503 Large-scale Data Structures And Organization

Assignment Help C/C++ Programming

Reference no: EM132839594

INF 503 Large-scale Data Structures And Organization - Northern Arizona University

Problem - Fun with direct access arrays

Create a class called FASTAreadset_DA. The purpose of the class will be to contain a FASTA read set (similar to homeworks #1 and #2) and all of the functions needed to operate on this set. Use the direct access hash table data-structure to store the genomic sequences of the given read dataset (hint: use an array of Boolean values - bool[] for your hash table). You will need to read in the genomic sequence fragments (feel free to ignore / discard all headers), covert them to a radix notation number (hint: try using an unsigned int to store the radix value), and flip the proper Boolean in the hash array to TRUE. If the Boolean is already "ON" (i.e. you are seeing a duplicate fragment), you'll need to record this ‘collision'.

At minimum, the class must contain:
• A constructor
• A destructor
• A function to search the hash table for a given 16-mer sequence
• A function to insert a given 16-mer sequence into the hash table
• Private variables to store the total # of collisions and # of elements stored in the array

A. Getting started: read in the read data set into your data structure
• What is the size of your hash table?
• How many collisions did you observe?
• How many unique sequences did you observe (number of "ON" Boolean values)?
• What is the load (αT) in your hash table?
B. Search time in direct access arrays: read in the genome sequence provided above, iterate through all 16-mers found in the genome, and use them to query the read set (similar to what you did in HW#2, problem 2B).
• How many genome 16-mer fragments were found in your read set?
• How long did it take to complete the entire search process (all 16-mers)?

Problem #2: The hash table with chaining
Create a class called FASTAreadset_Chain. Use the hash table data-structure to store the genomic sequences of the given read dataset (hint: you will need to provide the size of the hash table). If you have a duplicate sequence fragment or a duplicate hash value, use chaining method to resolve collisions. Resizing is optional - you can hard-code the proper hash table size through the constructor. Use Radix / division scheme for hash function implementation.
At minimum, the class must contain:
• A constructor
• A destructor
• A function to search the hash table for a given 16-mer sequence
• A function to insert a given 16-mer sequence into the hash table
• A private variable to set the hash table size
• A private variable to count the number of collisions during hash table creation

A. Assessing the impact of the hash table size. For this you will need to set the hash table to a fixed value (m, see below) and read in the read set to populate the hash table. Set the size of your hash table (m) to 10 thousand, 100 thousand, 1 million, and 10 million elements.
• For each of your 4 hash table sizes, how many collisions did you observe while populating the hash?
• For each of your 4 hash table sizes, how long did it take you to read the sequence fragment file?
• Do the results make sense? Explain.

B. Searching in the chain-linked hash table. Set the hash size to 10,000,000 and populate it using the read set. Read in the genome, iterate through all 16-mers found in the genome, and use them to query the read set (similar to what you did in HW#2, problem 2B).
• How many genome 16-mer fragments were found in your read set?
• How long did it take to complete the entire search process (all 16-mers)?
• How does that compare to the direct access array search times you've implemented as part of problem 1B?

Attachment:- Direct access arrays.rar

Reference no: EM132839594

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