From 97e0caa731262f2b81174d6aad3323b01733e571 Mon Sep 17 00:00:00 2001 From: Dmitry Kokorin Date: Tue, 1 Mar 2016 00:22:05 +0300 Subject: [PATCH] nucleotide_count: initial commit --- cpp/nucleotide-count/CMakeLists.txt | 52 +++++++++++ cpp/nucleotide-count/README.md | 63 ++++++++++++++ .../nucleotide_count_test.cpp | 86 +++++++++++++++++++ 3 files changed, 201 insertions(+) create mode 100644 cpp/nucleotide-count/CMakeLists.txt create mode 100644 cpp/nucleotide-count/README.md create mode 100644 cpp/nucleotide-count/nucleotide_count_test.cpp diff --git a/cpp/nucleotide-count/CMakeLists.txt b/cpp/nucleotide-count/CMakeLists.txt new file mode 100644 index 0000000..95c7011 --- /dev/null +++ b/cpp/nucleotide-count/CMakeLists.txt @@ -0,0 +1,52 @@ +# 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}) diff --git a/cpp/nucleotide-count/README.md b/cpp/nucleotide-count/README.md new file mode 100644 index 0000000..1ffcfe0 --- /dev/null +++ b/cpp/nucleotide-count/README.md @@ -0,0 +1,63 @@ +# Nucleotide Count + +Given a DNA string, compute how many times each nucleotide occurs in the string. + +DNA is represented by an alphabet of the following symbols: 'A', 'C', +'G', and 'T'. + +Each symbol represents a nucleotide, which is a fancy name for the +particular molecules that happen to make up a large part of DNA. + +Shortest intro to biochemistry EVAR: + +- twigs are to birds nests as +- nucleotides are to DNA and RNA as +- amino acids are to proteins as +- sugar is to starch as +- oh crap lipids + +I'm not going to talk about lipids because they're crazy complex. + +So back to nucleotides. + +DNA contains four types of them: adenine (`A`), cytosine (`C`), guanine +(`G`), and thymine (`T`). + +RNA contains a slightly different set of nucleotides, but we don't care +about that for now. + +## 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 DNA Nucleotides_problem at Rosalind [view source](http://rosalind.info/problems/dna/) diff --git a/cpp/nucleotide-count/nucleotide_count_test.cpp b/cpp/nucleotide-count/nucleotide_count_test.cpp new file mode 100644 index 0000000..73f0730 --- /dev/null +++ b/cpp/nucleotide-count/nucleotide_count_test.cpp @@ -0,0 +1,86 @@ +#include "nucleotide_count.h" +#define BOOST_TEST_MAIN +#include +#include + +namespace boost +{ + +// teach Boost.Test how to print std::pair +template +inline wrap_stringstream& +operator<<(wrap_stringstream& wrapped, std::pair const& item) +{ + return wrapped << '<' << item.first << ',' << item.second << '>'; +} + +} + +BOOST_AUTO_TEST_CASE(has_no_nucleotides) +{ + const dna::counter dna(""); + const std::map expected{ {'A', 0}, {'T', 0}, {'C', 0}, {'G', 0} }; + + const auto actual = dna.nucleotide_counts(); + + BOOST_REQUIRE_EQUAL_COLLECTIONS(expected.begin(), expected.end(), actual.begin(), actual.end()); +} + +#if defined(EXERCISM_RUN_ALL_TESTS) +BOOST_AUTO_TEST_CASE(has_no_adenosine) +{ + const dna::counter dna(""); + + BOOST_REQUIRE_EQUAL(0, dna.count('A')); +} + +BOOST_AUTO_TEST_CASE(repetitive_cytidine_gets_counts) +{ + const dna::counter dna("CCCCC"); + + BOOST_REQUIRE_EQUAL(5, dna.count('C')); +} + +BOOST_AUTO_TEST_CASE(repetitive_sequence_has_only_guanosine) +{ + const dna::counter dna("GGGGGGGG"); + const std::map expected{ {'A', 0}, {'T', 0}, {'C', 0}, {'G', 8} }; + + const auto actual = dna.nucleotide_counts(); + + BOOST_REQUIRE_EQUAL_COLLECTIONS(expected.begin(), expected.end(), actual.begin(), actual.end()); +} + +BOOST_AUTO_TEST_CASE(counts_only_thymidine) +{ + const dna::counter dna("GGGGTAACCCGG"); + + BOOST_REQUIRE_EQUAL(1, dna.count('T')); +} + +BOOST_AUTO_TEST_CASE(counts_a_nucleotide_only_once) +{ + const dna::counter dna("GGTTGG"); + + dna.count('T'); + + BOOST_REQUIRE_EQUAL(2, dna.count('T')); +} + +BOOST_AUTO_TEST_CASE(validates_nucleotides) +{ + const dna::counter dna("GGTTGG"); + + BOOST_REQUIRE_THROW(dna.count('X'), std::invalid_argument); +} + +BOOST_AUTO_TEST_CASE(counts_all_nucleotides) +{ + const dna::counter dna("AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC"); + std::map expected{ {'A', 20}, {'T', 21}, {'G', 17}, {'C', 12} }; + + auto actual = dna.nucleotide_counts(); + + BOOST_REQUIRE_EQUAL_COLLECTIONS(expected.begin(), expected.end(), actual.begin(), actual.end()); +} +#endif