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w1zeman1p's solution

to Hamming in the JavaScript Track

Published at Jul 13 2018 · 0 comments
Instructions
Test suite
Solution

Note:

This solution was written on an old version of Exercism. The tests below might not correspond to the solution code, and the exercise may have changed since this code was written.

Calculate the Hamming difference between two DNA strands.

A mutation is simply a mistake that occurs during the creation or copying of a nucleic acid, in particular DNA. Because nucleic acids are vital to cellular functions, mutations tend to cause a ripple effect throughout the cell. Although mutations are technically mistakes, a very rare mutation may equip the cell with a beneficial attribute. In fact, the macro effects of evolution are attributable by the accumulated result of beneficial microscopic mutations over many generations.

The simplest and most common type of nucleic acid mutation is a point mutation, which replaces one base with another at a single nucleotide.

By counting the number of differences between two homologous DNA strands taken from different genomes with a common ancestor, we get a measure of the minimum number of point mutations that could have occurred on the evolutionary path between the two strands.

This is called the 'Hamming distance'.

It is found by comparing two DNA strands and counting how many of the nucleotides are different from their equivalent in the other string.

GAGCCTACTAACGGGAT
CATCGTAATGACGGCCT
^ ^ ^  ^ ^    ^^

The Hamming distance between these two DNA strands is 7.

Implementation notes

The Hamming distance is only defined for sequences of equal length. This means that based on the definition, each language could deal with getting sequences of equal length differently.

Setup

Go through the setup instructions for JavaScript to install the necessary dependencies:

http://exercism.io/languages/javascript/installation

Running the test suite

The provided test suite uses Jasmine. You can install it by opening a terminal window and running the following command:

npm install -g jasmine

Run the test suite from the exercise directory with:

jasmine hamming.spec.js

In many test suites all but the first test have been marked "pending". Once you get a test passing, activate the next one by changing xit to it.

Source

The Calculating Point Mutations problem at Rosalind http://rosalind.info/problems/hamm/

Submitting Incomplete Solutions

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

hamming.spec.js

var Hamming = require('./hamming');

describe('Hamming', function () {
  var hamming = new Hamming();

  it('no difference between identical strands', function () {
    expect(hamming.compute('A', 'A')).toEqual(0);
  });

  xit('complete hamming distance for single nucleotide strand', function () {
    expect(hamming.compute('A', 'G')).toEqual(1);
  });

  xit('complete hamming distance for small strand', function () {
    expect(hamming.compute('AG', 'CT')).toEqual(2);
  });

  xit('small hamming distance', function () {
    expect(hamming.compute('AT', 'CT')).toEqual(1);
  });

  xit('small hamming distance in longer strand', function () {
    expect(hamming.compute('GGACG', 'GGTCG')).toEqual(1);
  });

  xit('large hamming distance', function () {
    expect(hamming.compute('GATACA', 'GCATAA')).toEqual(4);
  });

  xit('hamming distance in very long strand', function () {
    expect(hamming.compute('GGACGGATTCTG', 'AGGACGGATTCT')).toEqual(9);
  });

  xit('throws error when strands are not equal length', function () {
    expect(function () { hamming.compute('GGACGGATTCTG', 'AGGAC'); }).toThrow(
      new Error('DNA strands must be of equal length.')
    );
  });
});
function Hamming() {

}

Hamming.prototype.compute = function(strand1, strand2) {
    var difference = 0, i = 0;

    if(strand1.length != strand2.length) {
        throw Error('DNA strands must be of equal length.');
    }

    while(i < strand1.length) {
      if (strand1[i] !== strand2[i]) {
          difference++;
      }
      i++;
    }

    return difference;
};

module.exports = Hamming;

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