COMP2402 lab4

COMP2402 W24Lab4Specifications
Trees & HashSets & Maps (& Lists)
Prelab: due on brightspace by Friday March 8th, 3:00pm (no lates)
Programming: due on gradescope by Wednesday March 13th, 3:00pm (24h late ok)
Postlab: due on brightspace.ca by Wednesday March 20th, 3:00pm (no lates)
Topic focus: Lec 1- 15
Feedback on Lab 2 Feedback
Thank you very much to the 32 of you that took the time to fill out Lab 2 feedback. I was
planning on writing up a report like last time but Life got in the way. But I’ve carefully read over
your feedback and there were some common themes:
● Talk about iterators in lecture (will do next time! I mentioned their benefits in the
in-person section but maybe my videos do not. Note to self to add that in.)
● For any local test written after I read the Lab 2 Feedback, you’ll notice that the “Expect”
comment is now in the output text as well. I hope this reduces some of your pattern
matching time. Thanks for the suggestion, mystery student
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● Lab 2 took longer than Lab 1 (which is natural, but maybe some warning could be
given.) I can/should also emphasize how you should ask for help when you are stuck.
Our TAs are on piazza all. the. time. While during “deadline week” you might not get a
response right away, our average response time is 43 minutes. We’ve had over 600
posts in 6 weeks so we’ve been busy! You can’t see all the private posts we get, but if
you ask a question during “forum monitoring” times and you don’t get a response asap it
could be that the TA is busy responding to a bunch of other private posts.
● autograder: some issues remain although many of you appreciate getting feedback
before the deadline. Without the autograder you wouldn’t have any hints as to whether
you had a good data structure choice and since this course is about that choice, you
would have no idea whether your choice is good. But I know it can be frustrating to not
know where your bugs are. Sadly, this frustration will persist throughout your computer
science career in various ways. I will continue to work on naming the tests better.
Changes from Labs 1-3
The autograders have more structured feedback, so that it’s a bit better at being a “checkpoint.”
For example, many of the PhyloTree tests are for k=1, or when the Strings are not null, etc. You
can focus on these special cases first and then worry about more general cases, if you wish.
There are still no hidden tests. In a sense, the autograder variability serves as a “hidden test” in
that you sometimes have to look at your code and determine its complexity (gasp!) and decide
whether it matches the desired complexity rather than relying on the occasionally flaky tests.
Finally, I made this new flow chart to help you determine where your problems are and how to
communicate those problems to the course staff so that we can help you as quickly as possible!
Lab Objectives
The labs in this course are meant to give you the opportunity to practice with the topics of this
course in a way that is challenging yet also manageable. At times you may struggle and at
others it may seem more straight-forward; keep trying and practicing and you will improve.
Specifically, Lab 4 aims to improve your

1. Implementation Skills
   Implement iterative operations for tree-based data structures similar to the BinaryTree
   and BinarySearchTree (add, find, remove, iterate, traverse, rotations).
2. Design Skills
   Use object-oriented programming concepts such as abstraction and polymorphism to
   provide flexibility in your choices of which interface implementation to use.
3. Critical Thinking
   Demonstrate a solid understanding of the pros and cons of various implementations of
   the SSet (randomized, expected, worst-case) and of the situations when an unsorted set
   or map might be a better choice than a sorted set or list. This includes considering the
   time- and space-complexity of various operations in different data structures.
4. Algorithmic Thinking
   Apply algorithmic thinking to design efficient algorithms for common tree-based
   operations, such as find(x), iteration over nodes using pointers, careful pointer
   manipulation in tree rotations, and removing recursion to avoid a big call stack.
5. Error Handling
   Implement appropriate error handling and boundary checks to ensure the robustness of
   the data structures.
6. Testing
   Determine the necessary tests to ensure your algorithms are correct and efficient.
7. Planning
   Maintain or adopt good academic and programming habits through the pre-lab.
8. Reflection
   Reflect on your choice of data structures and algorithms through the post-lab.
   Assignment Components
   Details of each component follow later in the specifications.
9. (6.7 points) Prelab (complete on brightspace)
10. (80 points) Programming portion (submit on gradescope.ca)
    a. (50 points) PhyloTree Implementation
    b. (10 points) Genes implementation
    c. (10 points) GenesOrder Implementation
    d. (10 points) GenesCount implementation
11. (13.3 points) Postlab (complete on brightspace)
    Grading Criteria & Submission Guidelines
    See the Grading Criteria and Submission Guidelines of Lab 1; they are the same.
    Collaboration & Academic Integrity
12. Individual work is expected. Any collaboration should be explicitly mentioned and
    acknowledged at the top of each file. It is okay to discuss high-level approaches with
    your peers, or low-level syntax-type questions, but you must construct your solution
    on your own (as in: you have to formulate the code of your solution on your own.)
    Consider the analogy of writing an essay. You might talk with a peer about the high-level
    concepts of your thesis, or you might ask them about grammar or even phrasing of
    individual sentences. But you should not be writing the essay sentence-by-sentence with
    someone else’s help; in the end you have to sit down and write that thing on your own.
13. Plagiarism will result in severe consequences. Ensure that all code and
    documentation are your own work. Do not send code to or receive code from any
    source except for course staff or the textbook, even if you change a thing here or there.
    It helps to keep the analogy of an essay in mind; it is not okay to take a paragraph from
    a friend and then rearrange some of the words or replace some with a thesaurus. It’s not
    even okay to paraphrase each sentence. It is not okay to send your essay to a peer.
    Similarly here, you cannot start with code that is not yours and then “make it your own”
    with minor edits. Automated tools for detecting plagiarism will be employed in this
    course.
14. The same restrictions apply to AI programmers (such as chatGPT, copilot). You can
    use them to help with basic syntax (e.g. “spelling” and “grammar”) or to understand
    broad concepts (e.g. getting feedback on a thesis) but you have to formulate your
    solution in code on your own (e.g. you have to write that essay yourself.)
15. Note that contract cheating sites are known, unauthorized, and regularly monitored.
    Some of these services employ misleading advertising practices and have a high risk of
    blackmail and extortion.
16. Every student should be familiar with the Carleton University student academic integrity
    policy. Academic integrity is upheld in this course to the best of Prof Alexa’s abilities, as
    it protects the students that put in the effort to work on coursework within the allowable
    parameters. Potential violations must be reported to the Dean of Academic Integrity. If
    you ever have questions about what is or is not allowable regarding academic integrity,
    please do not hesitate to reach out to course staff. We are happy to answer.
    Copyright
    Prof Alexa is the exclusive owner of copyright and intellectual property of all course materials,
    including the labs. You may use course materials for your own educational use. You may not
    reproduce or distribute course materials publicly for commercial purposes, or allow others
    to, without express written consent.
    Workflow
    In a perfect world, this is how you would complete Lab 4:
17. Attend or watch the relevant lectures that are listed in the heading of this document.
18. Read the lab objectives listed on the second page of this document. For each data
    structure listed there, review its important algorithms as well as the time- and space
    complexity of its methods. This should give you some pros and cons for each.
19. Carefully read each problem detailed in the Programming section of this document.
    a. Make sure you understand the problem.
    b. Try the given examples by hand to get a better understanding of the problem.
    c. Pay special attention to any special cases or edge cases.
    d. Try more examples of your own devising if you need them.
    e. Donot start programming yet!
    f.
    Consider attending or watching the lab’s workshop video, posted on brightspace.
20. Once you have completed steps 1-3, you are ready to do the prelab (brightspace).
21. Complete the programming portion of the lab.
    a. Take this one problem at a time. Any order should be okay.
    b. Remember what you learned in Steps 1-4 as you brainstorm solutions.
    c. Test locally at frequent intervals. Do not write a whole program then test it
    afterwards. See the section on Local Tests to help you here.
    d. Submit to gradescope.ca whenever you have made good progress, but do not
    use gradescope.ca as your only tests. Gradescope keeps your most recent score
    unless you select a different submission to be active. See the section on the
    Gradescope Autograder to help you debug here.
    e. If you’re stuck on a problem for more than 30 minutes, ask for help using the How
    to Get Help section. Move on to something else until help has arrived.
22. Once the late programming deadline has passed, complete the post-lab (brightspace).
    a. If you did well on the programming portion, this is not meant to take too long.
    b. There are resources available to help you posted on brightspace under the Lab 2
    module. There is a solutions walk-through video for each part, and also a debrief
    document where I walk through the problem solving process and learning
    engagement I was hoping you would experience. You might consider looking at
    these before completing the prelab if you had trouble with any of the
    programming parts.
    c. You do not have to have completed the programming parts in order to do the
    postlab. If you were stuck on a problem, this is an opportunity to look at the
    sample solution videos, to figure out what went wrong for you, and to still learn
    what you were meant to learn.
    Coding Environment Setup
    Lab 1’s Coding Environment Setup will work with Lab 4 (replace Lab1/l1 with Lab4/l4). The
    file structure and many of the files will be the same, with new and different files as well.
    Programming Components
    Programming Notes
23. You may use java.util.HashSet instead of ods.MultiplicativeHashSet if you want the
    fastest implementation of a HashSet. Note that HashSet has an iterator.
24. You may use java.util.HashMap as well, for a fast implementation of a HashMap. Note
    that HashMap has an iterator over its keys or values.
25. If you want to use Collections.sort on an array-based Collection, you can!
    e.g. ArrayDeque ad = …
    Collections.sort(ad);
    // initialize ad etc
    // now ad is sorted!
    This takes O(n log n) time, where n is the number of elements in ad.
    You can also sort a Collection using a new comparison rule (a Comparator) , eg
    e.g. Collections.sort(ad,MyComp); // sort ad using MyComp
    where you may have defined MyComp elsewhere like this
    class MyComp implements Comparator {
    public int compare(String a, String b) {
    // Fill in compare
    }
    }
    Here are some examples on geeksforgeeks. Note that sorting a linked-list-based
    Collection can be done, but java first dumps the linked list into a structure with fast
    random access, and then sorts on that better structure, then dumps the sorted thing
    back into your linked-list-based structure. Keep that in mind, I suppose.
26. If you want to store objects of a class (of your own definition) in a sorted set, you need to
    ensure your class implements Comparable. For example, you could have
    class MyClass implements Comparable {
    int x;
    int y;
    public int compareTo(MyClass b) {
    // Fill in compareTo
    }
    }
    Here are some examples on geeksforgeeks.
27. Note that you should not need recursion for any of the problems. You can/should run all
    tests with the-Xss144k flag (or, the smallest heap size your local machine will allow.)
    Sometimes you’ll pass such tests even with recursion.
    Implementation Practice [50 marks]
    PhyloTree [50 marks]
    PhyloTree represents a tree of distinct Strings (where a String can ostensibly represent a DNA
    sequence; no biology knowledge necessary for the lab). Your task is to implement the described
    methods according to the specifications below, using the starter code and lecture to guide you.
    The provided implementations are incomplete and incorrect, but should be enough to compile
    and run the (failing) local and autograder tests.
    The data structure is a modified BinaryTree of Strings of some fixed length k, where each String
    is either null or of some length k>0 that is fixed for the given tree. The tree represents a
    “phylogenetic tree,” which is essentially a hypothesized family tree for DNA. When a node has
    value null it means we haven’t determined that ancestor in the tree yet. Each (non-null) String
    of the tree should be distinct and of length k.
    This is the general idea. Let’s get to some details.
    Inner Class
    Node
    (Represents a Node in our tree.)
    String s
    Node
    The String of length k in this Node, or null.
    parent, left, right Theparent, left child and right child of this Node.
    boolean mark
    Helpful node-specific boolean, used in LCA.
    boolean[] set
    Fields
    ● Node r
    ● int n
    ● int k
    Helpful node-specific set, used in computeSet.
    The root Node for the tree.
    The number of nodes in the tree.
    The length of non-null Strings in the tree, k>0.
    ● HashMap<String,Node> stringsToNodes A map from each non-null String
    stored
    in the Tree to the node that contains that String.
    Used to speed up various methods.
    Implemented Methods & Constructor
    ● PhyloTree()
    Initializes the fields so that this tree is empty and k = 1.
    ● PhyloTree(int k)
    Initializes the fields so that this tree is empty and initializes k to the parameter.
    ● public int size()
    Returns the number of nodes in the tree.
    ● public void clear()
    Clears the tree so that it contains no elements.
    ● public String toString()
    Returns a list-based String representation of the tree in in-order that is helpful for
    debugging purposes.
    ● public String prettyPrint()
    Returns a tree-like String representation of the tree that is helpful for debugging
    purposes. This is only useful for smaller trees; for larger trees with missing children it can
    misrepresent the tree so use it cautiously.
    ● public int height()
    Returns the first Node in an in-order traversal. Note that his is a recursive method so use
    it with caution.
    ● protected Node firstNode()
    Returns the first Node in an in-order traversal.
    ● protected Node nextNode(Node w)
    Returns the Node that follows w in an in-order traversal.
    ● public Iterator iterator()
    Returns an Iterator that iterates over the Strings of the tree in in-order order. Note
    that the Strings are not being stored in sorted order, so it may not appear sorted.
    Constructor & Methods For You to Implement
    Implement all the following methods without recursion.
    Don’t forget to update stringsToNodes when you add a non-null String to the PhyloTree!
    Use the examples from lecture (e.g. traverse2, size2, findLastNode) to guide you here.
    ● public boolean addChild(String parent, String child) throws
    IllegalArgumentException
    Adds a Node containing child as the child of the existing parent.
    If parent is null, adds child as new root, with existing root as its left child.
    If parent has no children, add child as a left child.
    If parent has left child, add child as a right child.
    Throws an IllegalArgumentException if parent already has 2 children.
    Throws an IllegalArgumentException if parent is not null and doesn’t exist.
    Throws an IllegalArgumentException if child is not null and already exists
    Throws an IllegalArgumentException if child is not null and its length is not k.
    If you’ve implemented addChild, it is a very good idea to test this locally and on the autograder
    before proceeding. If your addChild isn’t working, none of the other tests are likely to work.
    ● public PhyloTree(ArrayStack a) // Constructor
    Initializes the tree to contain the elements of a, where a contains the elements of the tree
    in “level order” (i.e. a[0] is the root, a[1] and a[2] are the root’s children, and so forth.)
    Throws an IllegalArgumentException if non-null duplicates exist.
    Throws an IllegalArgumentException if any non-null String has length != k,
    where k is the length of the (non-null) Strings in a (they should all have same length.)
    If you’ve implemented PhyloTree, it is a very good idea to test this locally and on the
    autograder before proceeding. If this constructor isn’t working, many of the tests that depend on
    this constructor will also fail.
    ● public String LCA(String s, String t)
    Returns the “least common ancestor” (LCA) of the nodes containing s and t.
    The LCA is the first ancestor that s and t have in common (the one farthest from root r).
    Throws an IllegalArgumentException if s or t are null or aren’t in the tree.
    Note: The Node class has a mark field that can help you keep track of, say, nodes
    you’ve seen. Just remember that if you “mark” a node, you should “unmark” it before you
    return from LCA otherwise it will be “marked” the next time you call it.
    Hint: break your code into manageable parts. Perhaps separate out the logic of checking
    for exceptions from finding the nodes that contain s and t from the logic that find the
    LCA of those nodes.
    ● public void fixUp(String s)
    Performs a series of single rotations involving s until s is in a “good spot.”
    In particular, if the node containing s is not in “binary search tree” order relative to its
    parent (e.g. it’s a left child greater than its parent, or a right child less than its parent),
    use the appropriate single rotation to swap the parent-child relationship.
    Proceed up the tree as necessary until s is “good” relative to its parent.
    If s’s parent is null, it is in a “good spot”.
    Note that the rest of the tree may be completely disordered; that’s okay.
    Throws an IllegalArgumentException if s is null or is not in the tree.
    Hint: single rotations come up in Treaps and BinaryHeaps; look there for guidance.
    ● public void computeSets(int index)
    For this problem, each Node can hold a String of length k of DNABases (or is null).
    (You can use the provided class field DNABases = {A,C,G,T} here.)
    Initially, all the leaves will be non-null; the internal nodes may or may not be null.
    The given index indicates which index of the length-k String is relevant.
    This problem asks you to compute each node’s set of possible bases for the given index.
    You’ll use the node’s set field for this:
    i.e. if DNABases[b] is a possible base for the given index of node u, you’ll set
    u.set[b] = true
    (ex: if (index index) of u can be A,G then u.set=[true,false,true,false])
    Throws an IllegalArgumentException if the index<0 or index>=k.
    Throws an IllegalArgumentException if any of the leaves are null.
    Use the following algorithm to compute the sets:
    for each node v in post-order (working from leaves upwards)
    if v is a leaf
    v’s base is v’s character at given index
    else if v has one child c
    v’s set of bases is c’s set of bases
    else
    if v’s left and right children have overlapping sets
    v’s set= the overlap/intersection of left &
    right
    else (the sets do not overlap)
    v’s set = the combination/union of left & right
    Note: there are some methods for debugging and testing that will be helpful:
    setToBases(Node u)- returns a String representation of node u’s set
    allSets()- returns an ArrayStack of all node’s u’s sets, in post-order
    Desired Complexity
    In the following table, let
    ● ndenotethe number of nodes in our tree;
    ● d(s,t)denote the length of the path between nodes s and t
    ● rotations denotes the maximum number of rotations needed to fix u (which in the
    worst-case could be the length of the root → u path, but in best case could be O(1))
    marks method time complexity (extra) space
    complexity
    10 add(p,c) O(1)E O(1)
    10 PhyloTree(a) O(n) O(n)
    10 LCA(s,t) O(d(s,t)) O(1)
    10 fixUp(u) O(rotations) O(1)
    10 computeSets(index) O(n) O(1)
    Examples
    addChild
    Tree (pre) k method Tree(post)
    A 1 addChild(A,B) A
    B
    A
    B
    1 addChild(A,C) A
    B C
    A
    B
    1 addChild(B,C) A
    B
    C
    AA
    BB CC
    2 addChild(CC,DD) AA
    BB CC
    DD
    AA
    BB CC
    2 addChild(CC,null) AA
    BB CC
    null
    A
    B C
    1 addChild(null,D) D
    A
    B C
    A
    B C
    1 addChild(A,D) IllegalArgumentException
    (parent already has 2 children)
    A
    B C
    1 addChild(B,C) IllegalArgumentException
    (child already exists)
    A
    B C
    1 addChild(D,E) IllegalArgumentException
    (parent not found)
    A
    B C
    1 addChild(B,DD) IllegalArgumentException
    (child is not of length k)
    PhyloTree
    method Tree (post) k n
    PhyloTree(A,B) A
    B
    1 2
    PhyloTree(B,A) B
    A
    1 2
    PhyloTree(A,B,C,D) A
    B C
    D
    1 4
    PhyloTree(null,null,AA, BB, CC) null
    null AA
    BB CC
    2 5
    PhyloTree(A,B,C,D,E,F,G,H,null) A
    B C
    D E F G
    H null
    1 9
    PhyloTree(A,A) IllegalArgumentException
    (duplicate element}
    PhyloTree(A,BB) IllegalArgumentException
    (A and BB have different lengths)
    LCA
    Tree k method output
    A 1 LCA(A,A) A
    A
    B
    1 LCA(A,B) A
    A
    B
    1 LCA(B,B) B
    AA
    BB CC
    2 LCA(BB,CC) AA
    A
    B C
    1 LCA(D,C) A
    D E
    A
    B C
    D E
    1 LCA(D,E) B
    A
    B C
    D E
    1 LCA(E,A) A
    null
    B C
    D E
    1 LCA(E,C) null
    A
    B C
    1 LCA(A,D) IllegalArgumentException
    (input D not in the tree)
    A
    B C
    1 LCA(D,null) IllegalArgumentException
    (input cannot be null)
    A
    B C
    1 LCA(B,DD) IllegalArgumentException
    (input DD is not in the tree)
    fixUp
    Tree (pre) method Tree(post)
    A
    B
    fixUp(A) A
    B
    null
    B
    fixUp(B) null
    B
    A
    B
    fixUp(B) B
    A
    A
    B
    C
    fixUp(B) B
    A
    C
    A
    B
    C
    fixUp© C
    A
    B
    C
    B A
    fixUp(A) A
    C
    B
    D
    A B
    C
    fixUp© C
    D B
    A
    A
    B C
    fixUp(null) IllegalArgumentException
    (input is null)
    A
    B C
    fixUp(D) IllegalArgumentException
    (input not in tree)
    A
    B C
    addChild(D,E) IllegalArgumentException
    (parent not found)
    A
    B C
    addChild(B,DD) IllegalArgumentException
    (child is not of length k)
    computeSets
    Tree (pre) k method Tree with Sets
    AT 2 computeSets(0) AT[A]
    AT 2 computeSets(1) AT[T]
    null
    AC AG
    2 computeSets(0) null[A] (intersection)
    AC[A] AG[A]
    null
    A C
    1 computeSets(0) null[A,C] (union)
    A[A] C[C]
    TT
    CC GG
    AC CA AT GT
    2 computeSets(0) TT[A]
    CC[A,C] GG[A,G]
    AC[A] CA[C] AT[A] GT[G]
    A
    C
    1 computeSets(0) A[C]
    C[C]
    A
    G T
    1 computeSets(1) IllegalArgumentException
    (index >= k)
    A
    G null
    1 computeSets(0) IllegalArgumentException
    (leaf is null)
    Interface Practice [30 marks]
    Genes, Revisited
    In lab 3 the Genes problem asked you to compute the number of different strands of length k
    encountered in the input. This problem is similar in many ways, so I recommend you first review
    a sample solution (yours or ours) or the debrief before tackling this problem.
    Method Signature
    public static int genes(InputGenerator gen, int k)
    Method Behaviour
    Decodes each gene (substrand) of length k > 0 in the sequence generated by a given
    InputGenerator as follows, then returns the number of different decodings:
    For gene consisting of input characters cici+1ci+2. … .ci+k-1 we decode it as
    i·ci + (i+1)·ci+1 + (i+2)·ci+2 + … + (i+k-1)·ci+k-1
    Desired Complexity & Notes
    O(n)E time, where n is the number of characters generated.
    O(k+d)E space, where k is the integer input parameter, and d is the solution.
    ● Since there are 4 bases, d ≤ 4k and thus log d = O(k).
    ● Forreference, in Java, A=65, C=67, G=71, U=85.
    ● For large n and k, it’s conceivable your decoding will have integer overflow. That’s okay,
    let it overflow. The tests will overflow as well, which is simpler than describing ways to
    prevent overflow.
    Examples
    characters generated
    by gen
    AAAA
    AAAAU
    k
    decoding of individual
    characters
    3 [A·0,A·1,A·2,A·3]
    [0,65,130,195]
    3 [0,65,130,195,340
    ]
    different decodings
    [195,390]
    output
    (d)
    2
    n
    4
    [195,390,665]
    UGCGAAUAUA
    UUUUCCCCAAAA
    3 [0,71,134,213,260,
    325,510,455,680,58
    5]
    [205,418,607,
    798,1095,1290,
    1645,1720]
    12 [0,85,170,255,268
    ,335,402,469,520,
    585,650,715]
    [4454]
    3
    8
    1
    5
    10
    12
    UUUUCCCCAAA
    12 [0,85,170,255,268
    ,335,402,469,520,
    585,650]
    … c64CGAc68… 1 […,
    C·65,G·66,A·67,…
    ]
    (no chars)
    Testing & Autograder

0
[]
[…, 4355, …]
[]
0
<n
0
11
n
0
There are limited local tests in Genes.main and tests/GenesTest.java; see Lab 1 for
testing instructions. Submit Genes.java to gradescope; see Lab 1 for submission instructions.
GenesOrder, Revisited
Method Signature
public static AbstractList genesOrder(InputGenerator
gen, int k)
Method Behaviour & Notes
Returns a list of the different genes (substrands) of length k > 0 in the sequence generated by
a given InputGenerator, in sorted order.
An AbstractList is an abstract java interface that is implemented by all the ods List implementations
(e.g. ArrayStack, ArrayDeque, DLList, SkiplistList, etc). Using AbstractList as the return type
means you have the flexibility to choose which of these List implementations best suits your code
and the desired complexity requirements.
Desired Complexity & Notes
O(k2n)A time, where n is the number of characters generated.
O(kd) space, where k is the integer input parameter, and d is the solution.
Since there are 4 bases, d ≤ 4k and thus log d = O(k).
Examples
characters generated by gen
k
output
AAAA
AUAAA
3
3
AAA
AAA,AUA,UAA
n
4
5
UGCGAAUAUA
UUUUCCCCAAAA
Testing & Autograder
3
12
(no characters)
AAU,AUA,CGA,GAA,GCG,UAU,UGC 10
UUUUCCCCAAAA
0 0
12
0
There are limited local tests in GenesOrder.main and tests/GenesOrderTest.java; see
Lab 1 for testing instructions. Submit GenesOrder.java to gradescope; see Lab 1 for
submission instructions.
GenesCount
Method Signature
public static AbstractList genesCount(InputGenerator
gen, int k)
Method Behaviour & Notes
Returns a list of the different genes (substrands) of length k > 0 in the sequence generated by
a given InputGenerator, in order from most frequent to least frequent. When multiple genes have
the same frequency, order them alphabetically.
Desired Complexity & Notes
O(k(n+d log d))AE = O(k(n+kd))AE time.
O(kd) space.
Note: n is the number of characters generated, k is the parameter, and d is the solution.
Since there are 4 bases, d ≤ 4k and thus log d = O(k).
Examples
characters generated by gen
AAAA
k
3
output (d)
AAA
n
4
AUAAA
AUAAUAA
UGCGAAUAUA
UUUUCCCCAAAA
3
3
3
12
(no characters)
0
AAA,AUA,UAA
AUA,UAA,AAU
AUA,AAU,CGA,GAA,GCG,UAU,UGC
UUUUCCCCAAAA
5
5
10
12
0
Testing & Autograder
There are limited local tests in GenesCount.main and tests/GenesCountTest.java; see
Lab 1 for testing instructions. Submit GenesCount.java to gradescope; see Lab 1 for
submission instructions.
Local Tests
See the Local Tests section of Lab 1; be sure to replace comp2402w24l1 with
comp2402w24l4
Gradescope Autograder
See the Gradescope Autograder section of Lab 1; be sure to replace Lab 1 with Lab 4 where
necessary.
How to Get Help
See the How to Get Help section of Lab 1. It will be updated with any new resources rather than
duplicating information here.
Common Errors & Fixes
See the Common Errors & Fixes section of Lab 1. It will be updated with any new errors rather
than duplicating information here.
Glossary
There is a glossary at the top of the Problem Solving & Programming Tips document. If you
can’t find a term listed there, please post publicly on piazza so that everyone can benefit from
the answer!
Autograder Runtimes for Sample Solutions
To give you a sense for the autograder runtimes for “perfect scores” you can see some of the
screenshots that follow.
addChild
PhyloTree
LCA
fixUp
computeSets
Genes
GenesOrder
GenesCoun