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ahalls's solution

to Nucleotide Count in the Objective-C Track

Published at Jul 13 2018 · 3 comments
Instructions
Test suite
Solution

Given a single stranded DNA string, compute how many times each nucleotide occurs in the string.

The genetic language of every living thing on the planet is DNA. DNA is a large molecule that is built from an extremely long sequence of individual elements called nucleotides. 4 types exist in DNA and these differ only slightly and can be represented as the following symbols: 'A' for adenine, 'C' for cytosine, 'G' for guanine, and 'T' thymine.

Here is an analogy:

  • twigs are to birds nests as
  • nucleotides are to DNA as
  • legos are to lego houses as
  • words are to sentences as...

Setup

There are two different methods of getting set up to run the tests with Objective-C:

  • Create an Xcode project with a test target which will run the tests.
  • Use the ruby gem objc as a test runner utility.

Both are described in more detail here: http://exercism.io/languages/objective-c

Submitting Exercises

When submitting an exercise, make sure your solution file is in the same directory as the test code.

The submit command will look something like:

exercism submit <path-to-exercism-workspace>/objective-c/nucleotide-count/NucleotideCount.m

You can find the Exercism workspace by running exercism debug and looking for the line beginning with Workspace.

Source

The Calculating DNA Nucleotides_problem at Rosalind http://rosalind.info/problems/dna/

Submitting Incomplete Solutions

It's possible to submit an incomplete solution so you can see how others have completed the exercise.

NucleotideCountTest.m

#import <XCTest/XCTest.h>

#if __has_include("NucleotideCountExample.h")
# import "NucleotideCountExample.h"
# else
# import "NucleotideCount.h"
#endif

NS_ASSUME_NONNULL_BEGIN

@interface NucleotideCountTest : XCTestCase

@end

@implementation NucleotideCountTest

- (void)testEmptyDNAStringHasNoAdenosine {
  NucleotideCount *dna = [[NucleotideCount alloc] initWithStrand:@""];
  NSUInteger result = [dna count:@"A"];
  NSUInteger expected = 0;
  XCTAssertEqual(expected,result);
}

- (void)testEmptyNucleotideCountStringHasNoNucleotides {
  NucleotideCount *dna = [[NucleotideCount alloc] initWithStrand:@""];
  NSDictionary<NSString *, NSNumber *> *results = [dna nucleotideCounts];
  NSDictionary<NSString *, NSNumber *> *expected = @{ @"A": @0, @"T" : @0, @"C" : @0, @"G" : @0 };
  XCTAssertEqualObjects(results, expected);
}

- (void)testRepetitiveCytidineGetsCounted {
  NucleotideCount *dna = [[NucleotideCount alloc] initWithStrand:@"CCCCC"];
  NSUInteger result = [dna count:@"C"];
  NSUInteger expected = 5;
  XCTAssertEqual(expected,result);
}

- (void)testRepetitiveSequenceHasOnlyGuanosine {
  NucleotideCount *dna = [[NucleotideCount alloc] initWithStrand:@"GGGGGGGG"];
  NSDictionary<NSString *, NSNumber *> *results = [dna nucleotideCounts];
  NSDictionary<NSString *, NSNumber *> *expected = @{ @"A": @0, @"T" : @0, @"C" : @0, @"G" : @8 };
  XCTAssertEqualObjects(results, expected);
}

- (void)testCountsByThymidine {
  NucleotideCount *dna = [[NucleotideCount alloc] initWithStrand:@"GGGGGTAACCCGG"];
  NSUInteger result = [dna count:@"T"];
  NSUInteger expected = 1;
  XCTAssertEqual(expected,result);
}

- (void)testCountsANucleotideOnlyOnce {
  NucleotideCount *dna = [[NucleotideCount alloc] initWithStrand:@"CGATTGGG"];
  NSUInteger result = [dna count:@"T"];
  NSUInteger expected = 2;
  XCTAssertEqual(expected,result);
}

- (void)testValidatesNucleotideCount {
  XCTAssertThrows([[NucleotideCount alloc] initWithStrand:@"John"]);
}

- (void)testCountsAllNucleotides {
  NSString *longStrand = @"AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC";
  NucleotideCount *dna = [[NucleotideCount alloc] initWithStrand:longStrand];
  NSDictionary<NSString *, NSNumber *> *results = [dna nucleotideCounts];
  NSDictionary<NSString *, NSNumber *> *expected = @{ @"A": @20, @"T" : @21, @"C" : @12, @"G" : @17 };
  XCTAssertEqualObjects(results, expected);
}

@end
NS_ASSUME_NONNULL_END
//
//  NucleotideCount.m
//  Created by Andrew Halls on 11/30/13.
//

#import "NucleotideCount.h"

@interface DNA ()

@property (nonatomic, strong) NSDictionary * nucleotideCounts;

@end


@implementation DNA


-(NSUInteger) count: (NSString *) nucleotide;
{
    [self validateNucleotide:nucleotide];
    return [ self.nucleotideCounts[nucleotide] integerValue];
}

-(NSDictionary *) nucleotideCounter: (NSString *) inputStrand {
    
    NSMutableDictionary * counters = [@{ @"A": @0, @"T" : @0, @"C" : @0, @"G" : @0 } mutableCopy];
    
    for (NSInteger index = 0; index < inputStrand.length; index ++ ) {
        NSString * nucleotide = [NSString stringWithFormat:@"%c", [inputStrand characterAtIndex:index]];
        [self validateNucleotide:nucleotide];
        counters[nucleotide] = @([counters[nucleotide] integerValue] + 1);
    }
    
    return [NSDictionary dictionaryWithDictionary:counters];
    
}

-(instancetype) initWithStrand: (NSString *) inputStrand {
    self = [super init];
    if (self) {
        self.nucleotideCounts = [self nucleotideCounter: inputStrand];
    }
    return self;
}

-(void) validateNucleotide: (NSString *) nuceotide {
   NSCharacterSet * validNuceoties =  [NSCharacterSet characterSetWithCharactersInString:@"ATCGU"];
    
    if (nuceotide.length != 1 ||
        ![validNuceoties characterIsMember:[nuceotide characterAtIndex:0]]) {
          @throw([NSException exceptionWithName:@"Request Error" reason:@"Invalid Nucleotide" userInfo:nil]);
    }
    
}



@end

Community comments

Find this solution interesting? Ask the author a question to learn more.
Avatar of ahalls
ahalls
Solution Author
commented over 7 years ago

Great suggestion @burtlo ... It also made me re-think what I was checking and use NSCharacterSet to express the idea that only certain characters are valid in this context ...

How do you make the gray boxes around the code in Markdown?

Thanks for adapting Exercism to support Objective-C !!!!

Avatar of burtlo

There is no test for a nuceotide being greater than length 1 but its a good addition. A minor type in the name nuceotide but nothing major with the code.

In markdown you use the backticks to make it appear with the grey boxes around it: nuceotide

Avatar of ahalls
ahalls
Solution Author
commented over 7 years ago

The length check is just defensive programming if an empty string is provided the characterAtIndex:0 method will crash. I was raised on the notion that your code must guard against input that crashes either with code or at least Asserts. It maybe over engineering because in a real system input validation may be elsewhere ...

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