Homework #3 C++ programming assignment

CSCI 335 
Homework #3
C++ programming assignment (100 points)
Due March 12, 11:00pm
This is an individual assignment
1. Please follow the Blackboard instructions on writing and submitting programming
assignments. The functions you provide should compile and run to receive any
credit.
2. Read and follow the contents Programming Rules document on Blackboard
(‘Course Information’ Section).
3. Read the assignment description below.
4. Submit only the files requested in the deliverables at the end of this document to
Gradescope by the deadline.
Learning Outcome: The goal of this assignment is to become familiar with lists and trees and
compare the performance of the self-balancing AVL tree. You will also work with a real-world data
set and construct a generic test routine for comparing several different implementations of the tree
container class. You are encouraged to use the book’s implementation for AVL trees. Acknowledge
the sources you use in the README.AVL file.
AVL Trees
Files provided: avl_tree.h, query_tree.cc, test_tree.cc, test_tree_mod.cc, dsexceptions.h, a
README.txt, a Makefile and more text (.txt) files. The output should look exactly as described below to
obtain the full grade (consider this part of an exact API specification).
Part 1 (15 points)
First, create a class object named SequenceMap that has as private data members the following two:
 string recognition_sequence_ ;
 vector<string> enzyme_acronyms_;
Other than the big-five (note that you can use the defaults for all of them), you have to add the
following:
a) A constructor SequenceMap(const string &a_rec_seq, const string &an_enz_acro),that
constructs a SequenceMap from two strings (note that after the constructor is called the vector
enzyme_acronyms_ will contain just one element, the an_enz_acro).
b) bool operator<(const SequenceMap &rhs) const, that operates based on the regular string
comparison between the recognition_sequence_ strings (this will be a one line function).
c) Overload the << operator in order to print out the enzyme_acronyms vector, for a given
recognition sequence. Refer to assignment 1 for example of overloading the operator signature.
d) void Merge(const SequenceMap &other_sequence). This function assumes that the object’s
recognition_sequence_ and other_sequence.recognition_sequence_ are equal to each other. The
function Merge() merges the other_sequence.enzyme_acronym_ with the object’s
enzyme_acronym_. The other_sequence object will not be affected.
This class (which is non-templated) will be used in the following programs. First test it with your own
test functions to make sure that it operates correctly.
Part 2
Introduction to the problem
For this assignment you will receive as input two text files, rebase210.txt and sequences.txt. After the
header, each line of the database file rebase210.txt contains the name of a restriction enzyme and
possible DNA sites the enzyme may cut (cut location is indicated by a ‘) in the following format:
enzyme_acronym/recognition_sequence/…/recognition_sequence//
For instance the first few lines of rebase210.txt are:
AanI/TTA'TAA//
AarI/CACCTGCNNNN'NNNN/'NNNNNNNNGCAGGTG//
AasI/GACNNNN'NNGTC//
AatII/GACGT'C//
AbsI/CC'TCGAGG//
AccI/GT'MKAC//
AccII/CG'CG//
AccIII/T'CCGGA//
Acc16I/TGC'GCA//
Acc36I/ACCTGCNNNN'NNNN/'NNNNNNNNGCAGGT//
…
That means that each line contains one enzyme acronym associated with one or more recognition
sequences. For example on line 2:
The enzyme acronym AarI corresponds to the two recognition sequences CACCTGCNNNN'NNNN and
'NNNNNNNNGCAGGTG.
Part 2.1 (25 points)
You will create a parser to read in this database and construct an AVL tree. For each line of the database
and for each recognition sequence in that line, you will create a new SequenceMap object that contains
the recognition sequence as its recognition_sequence_ and the enzyme acronym as the only string of its
enzyme_acronyms_, and you will insert this object into the tree. This is explained with the following
pseudo code:
Tree<SequenceMap> a_tree;
string db_line;
// Read the file line-by-line:
while (GetNextLineFromDatabaseFile(db_line)) {
 // Get the first part of the line:
 string an_enz_acro = GetEnzymeAcronym(db_line);
 string a_reco_seq;
 while (GetNextRecognitionSequence(db_line, a_rego_seq){
SequenceMap new_sequence_map(a_reco_seq, an_enz_acro);
a_tree.insert(new_sequence_map);
 } // End second while.
} // End first while.
In the case that the new_sequence_map.recognition_sequence_ equals the recognition_sequence_ of a
node X in the tree, then the search tree’s insert() function will call the X.Merge(new_sequence_map)
function of the existing element. This will have the effect of updating the enzyme_acronym_ of X. Note,
that this will be part of the functionality of the insert() function. The Merge() will only be called in case
of duplicates as described above. Otherwise, no Merge() is required and the new_sequence_map will be
inserted into the tree.
To implement the above, write a test program named query_tree which will use your parser to
create a search tree and then allow the user to query it using a recognition sequence. If that sequence
exists in the tree then this routine should print all the corresponding enzymes that correspond to that
recognition sequence.
Your programs should run from the terminal as follows:
% ./query_tree <database file name>
For example you can write on the terminal:
% ./query_tree rebase210.txt
The user should enter THREE strings (supposed to be recognition sequences) for instance:
CC'TCGAGG
TTA'TAA
TC'C
Your program should print in the standard output their associated enzyme acronyms. In the above
example the output will be
AbsI
AanI PsiI
Not Found
We will test it with a file containing three strings and run your code like that:
% ./query_tree rebase210.txt < input_part2.1.txt
Part 2b (20 points)
Next, create a test routine named test_tree that does the following in the sequence described below:
1. Parses the database and construct a search tree (this is the same as in Part 2.1).
2. Prints the number of nodes in your tree �.
3. Computes the average depth of your search tree, i.e. the internal path length divided by �.
a. Prints the average depth.
b. Prints the ratio of the average depth to log! �. E.g., if average depth is 6.9 and log! � =
5.0, then you should print ".$
%.& = 1.38.
4. Searches (find()) the tree for each string in the sequences.txt file and counts the total number
of recursive calls for all executions of find().
a. Prints the total number of successful queries (number of strings found).
b. Prints the average number of recursion calls, i.e. #total number of recursion calls /
number of queries.
5. Removes every other sequence in sequences.txt from the tree and counts the total number of
recursion calls for all executions of remove().
a. Prints the total number successful removes.
b. Prints the average number of recursion calls, i.e. #total number of recursion calls /
number of remove calls.
6. Redo steps 2 and 3:
a. Prints number of nodes in your tree.
b. Prints the average depth.
c. Prints the ratio of the average depth to log! �.
The output of Part2(b) should be of the exact form:
2: <integer>
3a: <float>
3b: <float>
4a: <integer>
4b: <float>
5a: <integer>
5b: <float>
6a: <integer>
6b: <float>
6c: <float>
If you didn’t complete a step, just print after the step number: Not Done
Your program should run from the terminal as follows:
% ./test_tree <database file name> <query file name>
For example you can write on terminal
% ./test_tree rebase210.txt sequences.txt
Part 2.3 (15 points)
You will use the avl_tree.h code you have written for Part 2.2 and you will modify it in order to
implement double rotations directly instead of calling the two single rotations. Name your modified
implementation avl_tree_mod.h. Run the exact same routines as in Part 2.2, but now with your
modified AVL implementation. The executable should be named test_tree_mod. The results should be
the same as in Part 2.2.
For example you can write on terminal
% ./test_tree_mod rebase210.txt sequences.txt
You will be given a mandatory Makefile, along with some code to start (start of main functions)
query_tree.cc test_tree.cc test_tree_mod.cc
Gradescope Deliverables: You should only submit these files:
• README.AVL file
• Part 1:
sequence_map.h: Your original sequence_map.h will be reused for all further sections.
• Part 2.1: (Modify avl_tree code by adding functions)
query_tree.cc
avl_tree.h
• Part 2.2:
test_tree.cc
avl_tree.h
• Part 2.3:
test_tree_mod.cc
avl_tree_mod.h