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artemkorsakov's solution

to Hamming in the Java Track

Published at Feb 06 2019 · 0 comments
Instructions
Test suite
Solution

Note:

This exercise has changed since this solution was written.

Calculate the Hamming Distance between two DNA strands.

Your body is made up of cells that contain DNA. Those cells regularly wear out and need replacing, which they achieve by dividing into daughter cells. In fact, the average human body experiences about 10 quadrillion cell divisions in a lifetime!

When cells divide, their DNA replicates too. Sometimes during this process mistakes happen and single pieces of DNA get encoded with the incorrect information. If we compare two strands of DNA and count the differences between them we can see how many mistakes occurred. This is known as the "Hamming Distance".

We read DNA using the letters C,A,G and T. Two strands might look like this:

GAGCCTACTAACGGGAT
CATCGTAATGACGGCCT
^ ^ ^  ^ ^    ^^

They have 7 differences, and therefore the Hamming Distance is 7.

The Hamming Distance is useful for lots of things in science, not just biology, so it's a nice phrase to be familiar with :)

Implementation notes

The Hamming distance is only defined for sequences of equal length, so an attempt to calculate it between sequences of different lengths should not work. The general handling of this situation (e.g., raising an exception vs returning a special value) may differ between languages.

Java Tips

Hints

This is the first exercise with tests that require you to throw an Exception. Exceptions are typically thrown to indicate that a program has encountered an unexpected input or state.

We use JUnit's ExpectedException rule throughout the track to verify that the exceptions you throw are:

  1. instances of a specified Java type;
  2. (optionally) initialized with a specified message.

Running the tests

You can run all the tests for an exercise by entering

$ gradle test

in your terminal.

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.

HammingTest.java

import org.junit.Ignore;
import org.junit.Rule;
import org.junit.Test;
import org.junit.rules.ExpectedException;

import static org.junit.Assert.assertEquals;


public class HammingTest {

    @Rule
    public ExpectedException expectedException = ExpectedException.none();

    @Test
    public void testNoDistanceBetweenEmptyStrands() {
        assertEquals(0, new Hamming("", "").getHammingDistance());
    }

    @Ignore("Remove to run test")
    @Test
    public void testNoDistanceBetweenShortIdenticalStrands() {
        assertEquals(0, new Hamming("A", "A").getHammingDistance());
    }

    @Ignore("Remove to run test")
    @Test
    public void testNoDistanceBetweenLongIdenticalStrands() {
        assertEquals(0, new Hamming("GGACTGA", "GGACTGA").getHammingDistance());
    }

    @Ignore("Remove to run test")
    @Test
    public void testCompleteDistanceInSingleNucleotideStrand() {
        assertEquals(1, new Hamming("A", "G").getHammingDistance());
    }

    @Ignore("Remove to run test")
    @Test
    public void testCompleteDistanceInSmallStrand() {
        assertEquals(2, new Hamming("AG", "CT").getHammingDistance());
    }

    @Ignore("Remove to run test")
    @Test
    public void testSmallDistanceInSmallStrand() {
        assertEquals(1, new Hamming("AT", "CT").getHammingDistance());
    }

    @Ignore("Remove to run test")
    @Test
    public void testSmallDistanceInMediumStrand() {
        assertEquals(1, new Hamming("GGACG", "GGTCG").getHammingDistance());
    }

    @Ignore("Remove to run test")
    @Test
    public void testSmallDistanceInLongStrand() {
        assertEquals(2, new Hamming("ACCAGGG", "ACTATGG").getHammingDistance());
    }

    @Ignore("Remove to run test")
    @Test
    public void testNonUniqueCharacterInFirstStrand() {
        assertEquals(1, new Hamming("AAG", "AAA").getHammingDistance());
    }

    @Ignore("Remove to run test")
    @Test
    public void testNonUniqueCharacterInSecondStrand() {
        assertEquals(1, new Hamming("AAA", "AAG").getHammingDistance());
    }

    @Ignore("Remove to run test")
    @Test
    public void testSameNucleotidesInDifferentPositions() {
        assertEquals(2, new Hamming("TAG", "GAT").getHammingDistance());
    }

    @Ignore("Remove to run test")
    @Test
    public void testLargeDistanceInPermutedStrand() {
        assertEquals(4, new Hamming("GATACA", "GCATAA").getHammingDistance());
    }

    @Ignore("Remove to run test")
    @Test
    public void testLargeDistanceInOffByOneStrand() {
        assertEquals(9, new Hamming("GGACGGATTCTG", "AGGACGGATTCT").getHammingDistance());
    }

    @Ignore("Remove to run test")
    @Test
    public void testValidatesFirstStrandNotLonger() {
        expectedException.expect(IllegalArgumentException.class);
        expectedException.expectMessage("leftStrand and rightStrand must be of equal length.");

        new Hamming("AATG", "AAA");
    }

    @Ignore("Remove to run test")
    @Test
    public void testValidatesSecondStrandNotLonger() {
        expectedException.expect(IllegalArgumentException.class);
        expectedException.expectMessage("leftStrand and rightStrand must be of equal length.");

        new Hamming("ATA", "AGTG");
    }

}
class Hamming {
    private int distance = 0;

    Hamming(String leftStrand, String rightStrand) {
        if (leftStrand.length() != rightStrand.length()) {
            throw new IllegalArgumentException("leftStrand and rightStrand must be of equal length.");
        }
        calculateDistance(leftStrand, rightStrand);
    }

    int getHammingDistance() {
        return distance;
    }

    private void calculateDistance(String leftStrand, String rightStrand) {
        for (int i = 0; i < leftStrand.length(); i++) {
            if (leftStrand.charAt(i) != rightStrand.charAt(i)) {
                distance++;
            }
        }
    }

}

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