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php/hamming/README.md

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+# Hamming
+
+Write a program that can 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.
+
+## Making the Test Suite Pass
+
+1. Get [PHPUnit].
+
+        % wget --no-check-certificate https://phar.phpunit.de/phpunit.phar
+        % chmod +x phpunit.phar
+
+2. Execute the tests for an assignment.
+
+        % phpunit.phar wordy/wordy_test.php
+
+[PHPUnit]: http://phpunit.de
+
+
+## Source
+
+The Calculating Point Mutations problem at Rosalind [view source](http://rosalind.info/problems/hamm/)

php/hamming/hamming.php

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+<?php
+
+//
+// This is only a SKELETON file for the "Hamming" exercise. It's been provided as a
+// convenience to get you started writing code faster.
+//
+
+function distance($a, $b)
+{
+    //
+    // YOUR CODE GOES HERE
+    //
+}

php/hamming/hamming_test.php

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+<?php
+
+require "hamming.php";
+
+class HammingComparatorTest extends PHPUnit_Framework_TestCase
+{
+
+    public function testNoDifferenceBetweenIdenticalStrands()
+    {
+        $this->assertEquals(0, distance('A', 'A'));
+    }
+
+    public function testCompleteHammingDistanceOfForSingleNucleotideStrand()
+    {
+        $this->markTestSkipped();
+        $this->assertEquals(1, distance('A', 'G'));
+    }
+
+    public function testCompleteHammingDistanceForSmallStrand()
+    {
+        $this->markTestSkipped();
+        $this->assertEquals(2, distance('AG', 'CT'));
+    }
+
+    public function testSmallHammingDistance()
+    {
+        $this->markTestSkipped();
+        $this->assertEquals(1, distance('AT', 'CT'));
+    }
+
+    public function testSmallHammingDistanceInLongerStrand()
+    {
+        $this->markTestSkipped();
+        $this->assertEquals(1, distance('GGACG', 'GGTCG'));
+    }
+
+    public function testLargeHammingDistance()
+    {
+        $this->markTestSkipped();
+        $this->assertEquals(4, distance('GATACA', 'GCATAA'));
+    }
+
+    public function testHammingDistanceInVeryLongStrand()
+    {
+        $this->markTestSkipped();
+        $this->assertEquals(9, distance('GGACGGATTCTG', 'AGGACGGATTCT'));
+    }
+
+    public function testExceptionThrownWhenStrandsAreDifferentLength()
+    {
+        $this->markTestSkipped();
+        $this->setExpectedException('InvalidArgumentException', 'DNA strands must be of equal length.');
+        distance('GGACG', 'AGGACGTGG');
+    }
+}