hamming: initial commit

cpp/hamming/CMakeLists.txt

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+# Get the exercise name from the current directory
+get_filename_component(exercise ${CMAKE_CURRENT_SOURCE_DIR} NAME)
+
+# Basic CMake project
+cmake_minimum_required(VERSION 2.8.11)
+
+# Name the project after the exercise
+project(${exercise} CXX)
+
+# Locate Boost libraries: unit_test_framework, date_time and regex
+set(Boost_USE_STATIC_LIBS ON)
+set(Boost_USE_MULTITHREADED ON)
+set(Boost_USE_STATIC_RUNTIME OFF)
+find_package(Boost 1.55 REQUIRED COMPONENTS unit_test_framework date_time regex)
+
+# Enable C++11 features on gcc/clang
+if("${CMAKE_CXX_COMPILER_ID}" MATCHES "(GNU|Clang)")
+    set(CMAKE_CXX_FLAGS "-std=c++11")
+endif()
+
+# Configure to run all the tests?
+if(${EXERCISM_RUN_ALL_TESTS})
+    add_definitions(-DEXERCISM_RUN_ALL_TESTS)
+endif()
+
+# Get a source filename from the exercise name by replacing -'s with _'s
+string(REPLACE "-" "_" file ${exercise})
+
+# Implementation could be only a header
+if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/${file}.cpp)
+    set(exercise_cpp ${file}.cpp)
+else()
+    set(exercise_cpp "")
+endif()
+
+# Build executable from sources and headers
+add_executable(${exercise} ${file}_test.cpp ${exercise_cpp} ${file}.h)
+
+# We need boost includes
+target_include_directories(${exercise} PRIVATE ${Boost_INCLUDE_DIRS})
+
+# We need boost libraries
+target_link_libraries(${exercise} ${Boost_LIBRARIES})
+
+# Tell MSVC not to warn us about unchecked iterators in debug builds
+if(${MSVC})
+    set_target_properties(${exercise} PROPERTIES
+        COMPILE_DEFINITIONS_DEBUG _SCL_SECURE_NO_WARNINGS)
+endif()
+
+# Run the tests on every build
+add_custom_command(TARGET ${exercise} POST_BUILD COMMAND ${exercise})

cpp/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.
+
+## Getting Started
+
+Make sure you have read the [getting started with C++](http://help.exercism.io/getting-started-with-cpp.html)
+page on the [exercism help site](http://help.exercism.io/).  This covers
+the basic information on setting up the development environment expected
+by the exercises.
+
+## Passing the Tests
+
+Get the first test compiling, linking and passing by following the [three
+rules of test-driven development](http://butunclebob.com/ArticleS.UncleBob.TheThreeRulesOfTdd).
+Create just enough structure by declaring namespaces, functions, classes,
+etc., to satisfy any compiler errors and get the test to fail.  Then write
+just enough code to get the test to pass.  Once you've done that,
+uncomment the next test by moving the following line past the next test.
+
+```C++
+#if defined(EXERCISM_RUN_ALL_TESTS)
+```
+
+This may result in compile errors as new constructs may be invoked that
+you haven't yet declared or defined.  Again, fix the compile errors minimally
+to get a failing test, then change the code minimally to pass the test,
+refactor your implementation for readability and expressiveness and then
+go on to the next test.
+
+Try to use standard C++11 facilities in preference to writing your own
+low-level algorithms or facilities by hand.  [CppReference](http://en.cppreference.com/)
+is a wiki reference to the C++ language and standard library.  If you
+are new to C++, but have programmed in C, beware of
+[C traps and pitfalls](http://www.slideshare.net/LegalizeAdulthood/c-traps-and-pitfalls-for-c-programmers).
+
+## Source
+
+The Calculating Point Mutations problem at Rosalind [view source](http://rosalind.info/problems/hamm/)

cpp/hamming/hamming.cpp

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+#include "hamming.h"
+
+namespace hamming {
+
+int compute(const char *first, const char *second) {
+
+    return 0;
+}
+
+}

cpp/hamming/hamming.h

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+#pragma once
+
+namespace hamming {
+
+int compute(const char *first, const char *second);
+
+}

cpp/hamming/hamming_test.cpp

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+#include "hamming.h"
+#include <stdexcept>
+#define BOOST_TEST_MAIN
+#include <boost/test/unit_test.hpp>
+
+BOOST_AUTO_TEST_CASE(no_difference_between_identical_strands)
+{
+    BOOST_REQUIRE_EQUAL(0, hamming::compute("A", "A"));
+}
+
+#if defined(EXERCISM_RUN_ALL_TESTS)
+BOOST_AUTO_TEST_CASE(complete_hamming_distance_for_single_nucleotide_strand)
+{
+    BOOST_REQUIRE_EQUAL(1, hamming::compute("A", "G"));
+}
+
+BOOST_AUTO_TEST_CASE(complete_hamming_distance_for_small_strand)
+{
+    BOOST_REQUIRE_EQUAL(2, hamming::compute("AG", "CT"));
+}
+
+BOOST_AUTO_TEST_CASE(small_hamming_distance)
+{
+    BOOST_REQUIRE_EQUAL(1, hamming::compute("AT", "CT"));
+}
+
+BOOST_AUTO_TEST_CASE(small_hamming_distance_in_longer_strand)
+{
+    BOOST_REQUIRE_EQUAL(1, hamming::compute("GGACG", "GGTCG"));
+}
+
+BOOST_AUTO_TEST_CASE(domain_error_when_first_string_is_longer)
+{
+    BOOST_REQUIRE_THROW(hamming::compute("AAAG", "AAA"), std::domain_error);
+}
+
+BOOST_AUTO_TEST_CASE(domain_error_when_second_string_is_longer)
+{
+    BOOST_REQUIRE_THROW(hamming::compute("AAA", "AAAG"), std::domain_error);
+}
+
+BOOST_AUTO_TEST_CASE(large_hamming_distance)
+{
+    BOOST_REQUIRE_EQUAL(4, hamming::compute("GATACA", "GCATAA"));
+}
+
+BOOST_AUTO_TEST_CASE(hamming_distance_in_very_long_strand)
+{
+    BOOST_REQUIRE_EQUAL(9, hamming::compute("GGACGGATTCTG", "AGGACGGATTCT"));
+}
+#endif