Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

https://github.com/aaron-contreras/hamming-kata

Exercism.io java kata
https://github.com/aaron-contreras/hamming-kata

Last synced: 26 days ago
JSON representation

Exercism.io java kata

Awesome Lists containing this project

README 

        
# Hamming



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.



# Tips



## Hints



This is the first exercise with tests that require you to throw an

[`Exception`](https://docs.oracle.com/javase/8/docs/api/java/lang/Exception.html). `Exception`s are typically thrown to

indicate that a program has encountered an unexpected input or state.



We use JUnit's [`ExpectedException`](http://junit.org/junit4/javadoc/4.12/org/junit/rules/ExpectedException.html)

[rule](https://github.com/junit-team/junit4/wiki/rules) 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.



## Setup



Go through the setup instructions for Java to install the necessary

dependencies:



[https://exercism.io/tracks/java/installation](https://exercism.io/tracks/java/installation)



# Running the tests



You can run all the tests for an exercise by entering the following in your

terminal:



```sh

$ gradle test

```



> Use `gradlew.bat` if you're on Windows



In the test suites all tests but the first have been skipped.



Once you get a test passing, you can enable the next one by removing the

`@Ignore("Remove to run test")` annotation.



## Source



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