genesis::utils Namespace Reference

Namespaces
	details

Classes
class	ArrowOperatorProxy
	Proxy class to hold an element accessible via arrow operator. More...
class	AsynchronousReader
	Read bytes from an InputSource into a char buffer. More...
class	BadOptionalAccess
	Optional access error for empty values. More...
class	BaseInputSource
	Abstract base class for reading byte data from input sources. More...
class	BaseOutputTarget
	Abstract base class for writing data to an output target. More...
class	Bitvector
struct	BitvectorHash
	Helper structure that yields the hash of a given Bitvector. More...
struct	BitvectorXhash
	Helper structer that yields the x_hash of a given Bitvector. More...
class	BlockingConcurrentQueue
class	BmpWriter
	Write Bitmap image files. More...
class	CharLookup
	Simple lookup table providing a value lookup for each ASCII char (0-127). More...
class	Color
class	ColorMap
	Store a list of colors and offer them as a map for values in range [ 0.0, 1.0 ]. More...
class	ColorNormalization
	Base class for color normalization. More...
class	ColorNormalizationBoundary
	Color normalization that maps to discrete intervals. More...
class	ColorNormalizationDiverging
	Color normalization for a diverging scale. More...
class	ColorNormalizationLinear
	Default Color normalization, using a sequential linear scaling in the range [ min, max ]. More...
class	ColorNormalizationLogarithmic
	Color normalization for a logarithmic scale. More...
class	CompensatedSum
	Compensated summation algorithmm, such as Kahan, Neumaier, and Klein summation. More...
class	ConcurrentQueue
struct	ConcurrentQueueDefaultTraits
struct	ConsumerToken
class	CsvInputIterator
class	CsvReader
	Read Comma/Character Separated Values (CSV) data and other delimiter-separated formats. More...
class	Dataframe
class	DataframeReader
class	DereferenceIterator
	Iterator class that exposes elements in a container of pointers. More...
class	Deserializer
struct	EmptyGenericInputStreamData
	Empty helper data struct to serve as a dummy for GenericInputStream. More...
struct	EmptyIntervalData
	Empty class used as default for Interval data. More...
class	EuclideanKmeans
class	Exception
	Base class for genesis exceptions. More...
class	ExistingFileError
	Exception class that is thrown if trying to write to an existing file. More...
class	FileInputSource
	Input source for reading byte data from a file. More...
class	FileOutputTarget
	Output target for writing data to a file. More...
class	FilterIterator
	Iterator class that allows to filter an underlying iterator by skipping elements that do not satisfy a given predicate. More...
class	FunctionCache
	Simple cache, for example for function return values. More...
class	GenericInputStream
	Type erasure for iterators, using std::function to eliminate the underlying input type. More...
class	GeoCoordinate
	Geographical coordinates in degrees. More...
struct	GlmControl
struct	GlmExtras
struct	GlmFactor
struct	GlmFamily
struct	GlmFreedom
	Internal helper structure for GLMs to calcualte the residual degrees of freedom. More...
struct	GlmLink
struct	GlmOutput
class	GzipBlockOStream
	Output stream that writes blocks of gzip-compressed data to an underlying wrapped stream, using parallel compression. More...
class	GzipBlockOutputTarget
	Output target for writing byte data to a gzip-compressed target in blocks of gzip data. More...
class	GzipError
	Exception class thrown by failed gzip/zlib operations. More...
class	GzipIFStream
	Input file stream that offers on-the-fly gzip-decompression if needed. More...
class	GzipInputSource
	Input source for reading byte data from a gzip/zlib-compressed source. More...
class	GzipIStream
	Input stream that offers on-the-fly gzip-decompression if needed. More...
class	GzipOFStream
	Out file stream that offers on-the-fly gzip-compression. More...
class	GzipOStream
	Output stream that offers on-the-fly gzip-compression. More...
class	GzipOutputTarget
	Output target for writing byte data to a gzip/zlib-compressed target. More...
struct	hash
struct	hash< std::tuple< TT... > >
struct	HeatmapParameters
class	Histogram
	Histogram class for accumulating and summarizing data. More...
class	HistogramAccumulator
	Histogram helper class that collects data and builds a fitting Histogram. More...
struct	InfoCompiler
struct	InfoHardware
class	InputBuffer
class	InputStream
	Stream interface for reading data from an InputSource, that keeps track of line and column counters. More...
struct	Interval
	Type to store an interval (range) between two numbers, as used in the IntervalTree. More...
struct	IntervalClosed
	Helper type to define a closed [] Interval. More...
struct	IntervalLeftOpen
	Helper type to define a left open (] Interval. More...
struct	IntervalOpen
	Helper type to define an open () Interval. More...
struct	IntervalRightOpen
	Helper type to define a right open [) Interval. More...
class	IntervalTree
	Interval tree that enables storing and querying intervals, each containing some data. More...
class	IntervalTreeIterator
	Iterate the Intervals stored in an IntervalTree. More...
class	IntervalTreeNode
	Node in an IntervalTree. More...
class	IOError
	Exception class for general input/output errors. More...
class	IteratorDeletions
	Take a TwobitVector sequence and iterate over all possible deletions of its values. More...
class	IteratorInsertions
class	IteratorSubstitutions
class	JsonDocument
	Store a Json value of any kind. More...
class	JsonIterator
	Template for a random access iterator for the JsonDocument class. More...
class	JsonReader
	Read Json data into a JsonDocument. More...
class	JsonWriter
	Write Json data from a JsonDocument. More...
struct	KahanSummation
	Tag for tag dispatching the algorithm in CompensatedSum. See there for details. More...
struct	KleinSummation
	Tag for tag dispatching the algorithm in CompensatedSum. See there for details. More...
class	Kmeans
struct	KmeansClusteringInfo
	Helper POD that stores the variances and number of data points of each centroid, as well as the distances from all data points to their assigned centroids. More...
class	LightweightSemaphore
struct	LinearFunction
	Data structer to keep the two parameters of a linear function: its slope, and its intercept. More...
class	Logging
	Logging class with easy and fast usage. More...
struct	LoggingDetails
	POD stuct containing the settings for which information is included with each logging message. More...
class	LoggingScopeLevel
	Class that sets the Logging Level to a value von construction and set it back on destruction. This is used by the log scope level macro. More...
class	Matrix
class	MatrixCol
	View into a Matrix column. More...
class	MatrixReader
class	MatrixRow
	View into a Matrix row. More...
class	MatrixSimpleReader
class	MatrixWriter
class	MD5
	Calculate MD5 hashes for strings and files. More...
struct	MeanStddevPair
	Store a mean and a standard deviation value. More...
struct	MinMaxPair
	Store a pair of min and max values. More...
class	Moments
	Compute running mean and variance for an input. More...
class	MruCache
	Most Recently Used Cache. More...
class	MultiFuture
	Helper class to facilitate waiting for and/or getting the results of multiple futures at once. More...
struct	NaturalGreater
	Functor class to compare to strings with natural "human" sorting, see compare_natural(). More...
struct	NaturalLess
	Functor class to compare to strings with natural "human" sorting, see compare_natural(). More...
struct	NeumaierSummation
	Tag for tag dispatching the algorithm in CompensatedSum. See there for details. More...
class	NexusBlock
class	NexusDocument
class	NexusTaxa
class	NexusTrees
class	NexusWriter
struct	nullopt_t
	Type for nullopt. More...
class	Optional
	Simplistic optional: requires T to be default constructible, copyable. More...
class	Options
	Simple Options class for application-wide configuration and settings. More...
struct	PcaData
	Helper stucture that collects the output of principal_component_analysis(). More...
class	ProactiveFuture
	Wrapper around std::future that implements (pro-)active waiting, i.e., work stealing. More...
struct	ProducerToken
struct	Quartiles
	Store the values of quartiles: q0 == min, q1 == 25%, q2 == 50%, q3 == 75%, q4 == max. More...
class	Range
	Simple wrapper for typical begin() and end() iterators, to be used in range-based for loops. More...
class	RangeMinimumQuery
	Class that allows to efficiently find the index of the minimum element within an interval of an array of integer values. More...
class	ResourceLogger
class	SequentialOutputBuffer
	Buffer structure for output to be produced in a well-defined sequential order. More...
class	Serializer
class	SHA1
	Calculate SHA1 hashes for strings and files. More...
class	SHA256
	Calculate SHA256 hashes for strings and files. More...
class	StreamInputSource
	Input source for reading byte data from an istream. More...
class	StreamOutputTarget
	Output target for writing data to a stream. More...
class	StrictFStream
	Stream that defines a strict wrapper around std::fstream. More...
struct	StrictFStreamHolder
	Helper class template for managing the construction order between stream classes. More...
class	StrictIFStream
	Stream that defines a strict wrapper around std::ifstream. More...
class	StrictOFStream
	Stream that defines a strict wrapper around std::ofstream. More...
class	StringInputSource
	Input source for reading byte data from a string. More...
class	StringOutputTarget
	Output target for writing data to a string. More...
class	Style
	Simple text style class for colorized and bold output to a terminal. More...
struct	SvgAxisSettings
struct	SvgBox
struct	SvgCircle
struct	SvgColorBarSettings
class	SvgDefinitions
class	SvgDocument
struct	SvgDrawingOptions
struct	SvgEllipse
struct	SvgFill
struct	SvgFont
struct	SvgGradientLinear
struct	SvgGradientStop
struct	SvgGroup
struct	SvgImage
struct	SvgLine
struct	SvgMargin
struct	SvgMatrixSettings
class	SvgObject
struct	SvgPath
struct	SvgPoint
struct	SvgPolygon
struct	SvgPolyline
struct	SvgRect
struct	SvgSize
struct	SvgStroke
struct	SvgText
struct	SvgTransform
struct	SvgUse
class	SynchronousReader
	Read bytes from an InputSource into a char buffer. More...
class	Table
struct	TableLayout
class	ThreadCriticalSection
	Helper class to define a critical section. More...
class	ThreadPool
	Thread pool for distributed work. More...
class	ThreadsafeQueue
	Thread-safe queue. More...
struct	Tickmarks
	Helper class to find "nice" tickmark intervals for creating scales and axes. More...
class	TransformIterator
	Iterator class that allows to transform an underlying iterator by applying a function to each element before dereferencing. More...
struct	TridiagonalDecompositionData
	Helper structure used for the eigenvalue decomposition in reduce_to_tridiagonal_matrix() and tridiagonal_ql_algorithm(). See there for details. More...
class	TwobitVector
class	XmlComment
class	XmlDocument
class	XmlElement
class	XmlMarkup
class	XmlValue
class	XmlWriter
	Write Xml data. More...

Functions
template<typename T >
constexpr T	abs_diff (T const &lhs, T const &rhs)
	Calculate the absolute differenence between two values. More...
template<typename InputStream >
void	affirm_char_or_throw (InputStream &source, char criterion, SkipWhitespace skip_ws=SkipWhitespace::kNone)
	Lexing function that checks whether the current char from the stream equals the provided one. More...
template<typename InputStream >
void	affirm_char_or_throw (InputStream &source, std::function< bool(char)> criterion, SkipWhitespace skip_ws=SkipWhitespace::kNone)
	Lexing function that checks whether the current char from the stream fulfills the provided criterion. More...
template<class ForwardIterator >
double	aitchison_norm (ForwardIterator first, ForwardIterator last)
	Calculate the Aitchison norm of a range of positive numbers. More...
double	aitchison_norm (std::vector< double > const &vec)
	Calculate the Aitchison norm of a std::vector of double elements. More...
bool	almost_equal_relative (double lhs, double rhs, double max_rel_diff=std::numeric_limits< double >::epsilon())
	Check whether two doubles are almost equal, using a relative epsilon to compare them. More...
template<class ForwardIterator >
double	arithmetic_mean (ForwardIterator first, ForwardIterator last)
	Calculate the arithmetic mean of a range of numbers. More...
double	arithmetic_mean (std::vector< double > const &vec)
	Calculate the arithmetic mean of a std::vector of double elements. More...
template<typename T >
void	ascending (T &f, T &s)
	Sort two values in ascending order, inplace. More...
template<class T >
T	base64_decode_ (std::string const &input)
std::string	base64_decode_string (std::string const &input)
std::vector< std::uint8_t >	base64_decode_uint8 (std::string const &input)
std::string	base64_encode (std::string const &input, size_t line_length)
std::string	base64_encode (std::vector< std::uint8_t > const &input, size_t line_length)
template<class T >
std::string	base64_encode_ (T const &input, size_t line_length)
template<class ForwardIt , class T , class Compare = std::less<T>>
ForwardIt	binary_find (ForwardIt first, ForwardIt last, const T &value, Compare comp={})
	Binary search on a sorted/partitioned range, returns an iterator to the element if found. More...
double	binomial_coefficient (size_t n, size_t k)
	Compute the binomial coefficient, that is n choose k, for two integer numbers, for large numbers. More...
void	binomial_coefficient_check_n_k_ (size_t n, size_t k)
	Local helper function to check that n and k are valid for a binomial coefficient. More...
size_t	binomial_coefficient_int (size_t n, size_t k)
	Compute the binomial coefficient, that is n choose k, for two integer numbers. More...
double	binomial_distribution (size_t k, size_t n, double p)
	Compute the probability mass function for a binomial distribution. More...
std::string	bitstring (TwobitVector const &vec)
	Return a string with a bit-representation of a TwobitVector. More...
std::string	bitstring (TwobitVector::WordType const &vec)
	Return a string with a bit-representation of a TwobitVector::WordType. More...
Bitvector	bitwise_and (Bitvector const &lhs, Bitvector const &rhs, bool use_larger=false)
	Take the bitwise and of two Bitvectors of potentially different size. More...
Bitvector	bitwise_or (Bitvector const &lhs, Bitvector const &rhs, bool use_larger=false)
	Take the bitwise or of two Bitvectors of potentially different size. More...
Bitvector	bitwise_xor (Bitvector const &lhs, Bitvector const &rhs, bool use_larger=false)
	Take the bitwise xor of two Bitvectors of potentially different size. More...
static void	build_path_base_swap_ (std::string &path, const std::string &newbase)
constexpr bool	char_match_ci (char c1, char c2) noexcept
	Return whether two chars are the same, case insensitive, and ASCII-only. More...
std::string	char_to_hex (char c, bool full=true)
	Return the name and hex representation of a char. More...
std::string	char_to_hex (unsigned char c, bool full=true)
	Return the name and hex representation of a char, given as an unsigned char. More...
static std::string	chdir_getcwd_ (std::string const &dir)
static void	check_mode_ (std::string const &filename, std::ios_base::openmode mode)
static void	check_open_ (std::ios *s_p, std::string const &filename, std::ios_base::openmode mode)
static void	check_peek_ (std::istream *is_p, std::string const &filename, std::ios_base::openmode mode)
double	circumference (double radius)
template<class ForwardIterator >
void	closure (ForwardIterator first, ForwardIterator last)
	Calculate the closure of a range of numbers. More...
void	closure (std::vector< double > &vec)
	Calculate the closure of a std::vector of double elements. More...
double	coefficient_of_variation (MeanStddevPair const &ms)
	Calculate the index of dispersion. More...
std::vector< double >	coefficient_of_variation (std::vector< MeanStddevPair > const &ms)
	Calculate the index of dispersion. More...
Color	color_from_bytes (unsigned char r, unsigned char g, unsigned char b, unsigned char a=255)
	Create a Color given three or four values in the range [ 0, 255 ] for each of the components red, green and blue, and optionally alpha. More...
Color	color_from_hex (std::string const &hex_color, std::string const &prefix="#")
	Create a Color given a hex color string in the format "#003366[ff]". More...
Color	color_from_name (std::string const &name)
	Return the color represented by the given name, which is (currently) a shortcut for color_from_name_web() and color_from_name_xkcd(). More...
Color	color_from_name_lego (std::string const &name)
	Retrieve a named LEGO color by name. More...
Color	color_from_name_web (std::string const &name)
	Retrieve a named web color by name. More...
Color	color_from_name_xkcd (std::string const &name)
	Retrieve a named xkcd color by name. More...
std::vector< Color > const &	color_list_accent ()
	Color palette accent. More...
std::vector< Color > const &	color_list_blues ()
	Color palette blues. More...
std::vector< Color > const &	color_list_brbg ()
	Color palette brbg. More...
std::vector< Color > const &	color_list_bugn ()
	Color palette bugn. More...
std::vector< Color > const &	color_list_bupu ()
	Color palette bupu. More...
std::vector< Color > const &	color_list_bupubk ()
	Color Palette bupubk. More...
std::vector< Color > const &	color_list_dark2 ()
	Color palette dark2. More...
std::vector< Color > const &	color_list_diverging (ColorListDiverging palette)
std::vector< Color > const &	color_list_diverging (std::string const &palette)
std::vector< std::string >	color_list_diverging_names ()
std::vector< Color > const &	color_list_gnbu ()
	Color palette gnbu. More...
std::vector< Color > const &	color_list_greens ()
	Color palette greens. More...
std::vector< Color > const &	color_list_greys ()
	Color palette greys. More...
std::vector< Color > const &	color_list_heat ()
	Color palette heat. More...
std::vector< Color > const &	color_list_inferno ()
	Color palette inferno. More...
std::vector< Color > const &	color_list_magma ()
	Color palette magma. More...
std::vector< Color > const &	color_list_misc (ColorListMisc palette)
std::vector< Color > const &	color_list_misc (std::string const &palette)
std::vector< std::string >	color_list_misc_names ()
std::vector< Color > const &	color_list_nextstrain ()
	Color palette from the the Nextstrain build for novel coronavirus (nCoV) at https://nextstrain.org/ncov. More...
std::vector< Color >	color_list_nextstrain (size_t n)
	Color palette from the the Nextstrain build for novel coronavirus (nCoV) at https://nextstrain.org/ncov. More...
std::vector< Color > const &	color_list_oranges ()
	Color palette oranges. More...
std::vector< Color > const &	color_list_orrd ()
	Color palette orrd. More...
std::vector< Color > const &	color_list_paired ()
	Color palette paired. More...
std::vector< Color > const &	color_list_pastel1 ()
	Color palette pastel1. More...
std::vector< Color > const &	color_list_pastel2 ()
	Color palette pastel2. More...
std::vector< Color > const &	color_list_piyg ()
	Color palette piyg. More...
std::vector< Color > const &	color_list_plasma ()
	Color palette plasma. More...
std::vector< Color > const &	color_list_prgn ()
	Color palette prgn. More...
std::vector< Color > const &	color_list_pubu ()
	Color palette pubu. More...
std::vector< Color > const &	color_list_pubugn ()
	Color palette pubugn. More...
std::vector< Color > const &	color_list_puor ()
	Color palette puor. More...
std::vector< Color > const &	color_list_purd ()
	Color palette purd. More...
std::vector< Color > const &	color_list_purples ()
	Color palette purples. More...
std::vector< Color > const &	color_list_qualitative (ColorListQualitative palette)
std::vector< Color > const &	color_list_qualitative (std::string const &palette)
std::vector< std::string >	color_list_qualitative_names ()
std::vector< Color > const &	color_list_rdbu ()
	Color palette rdbu. More...
std::vector< Color > const &	color_list_rdgy ()
	Color palette rdgy. More...
std::vector< Color > const &	color_list_rdpu ()
	Color palette rdpu. More...
std::vector< Color > const &	color_list_rdylbu ()
	Color palette rdylbu. More...
std::vector< Color > const &	color_list_rdylgn ()
	Color palette rdylgn. More...
std::vector< Color > const &	color_list_reds ()
	Color palette reds. More...
std::vector< Color > const &	color_list_sequential (ColorListSequential palette)
std::vector< Color > const &	color_list_sequential (std::string const &palette)
std::vector< std::string >	color_list_sequential_names ()
std::vector< Color > const &	color_list_set1 ()
	Color palette set1. More...
std::vector< Color > const &	color_list_set2 ()
	Color palette set2. More...
std::vector< Color > const &	color_list_set3 ()
	Color palette set3. More...
std::vector< Color > const &	color_list_spectral ()
	Color palette spectral. More...
std::vector< Color > const &	color_list_viridis ()
	Color palette viridis. More...
std::vector< Color > const &	color_list_ylgn ()
	Color palette ylgn. More...
std::vector< Color > const &	color_list_ylgnbu ()
	Color palette ylgnbu. More...
std::vector< Color > const &	color_list_ylorbr ()
	Color palette ylorbr. More...
std::vector< Color > const &	color_list_ylorrd ()
	Color palette ylorrd. More...
std::vector< Color >	color_palette_lego ()
std::vector< Color >	color_palette_web ()
std::vector< Color >	color_palette_xkcd ()
std::map< double, Color >	color_stops (ColorMap const &map, ColorNormalization const &norm)
std::map< double, Color >	color_stops (ColorMap const &map, ColorNormalizationBoundary const &norm)
std::map< double, Color >	color_stops (ColorMap const &map, ColorNormalizationDiverging const &norm)
std::map< double, Color >	color_stops (ColorMap const &map, ColorNormalizationLinear const &norm)
std::map< double, Color >	color_stops (ColorMap const &map, ColorNormalizationLogarithmic const &norm)
std::map< double, std::string >	color_tickmarks (ColorNormalization const &norm, size_t num_ticks)
std::map< double, std::string >	color_tickmarks (ColorNormalizationBoundary const &norm, size_t num_ticks)
std::map< double, std::string >	color_tickmarks (ColorNormalizationDiverging const &norm, size_t num_ticks)
std::map< double, std::string >	color_tickmarks (ColorNormalizationLinear const &norm, size_t num_ticks)
std::map< double, std::string >	color_tickmarks (ColorNormalizationLogarithmic const &norm, size_t num_ticks)
std::string	color_to_hex (Color const &c, std::string const &prefix="#", bool uppercase=false, bool with_alpha=false)
	Return a hex string representation of a Color in the format "#003366[ff]". More...
constexpr std::size_t	combine_hashes (std::size_t h1, std::size_t h2)
	Combine two hash values. More...
constexpr std::size_t	combine_hashes_32 (std::size_t h1, std::size_t h2)
constexpr std::size_t	combine_hashes_64 (std::size_t h1, std::size_t h2)
int	compare_natural (std::string const &lhs, std::string const &rhs)
	Compare two strings with natural human sorting, that is "A1", "A2", "A100", instead of the standard sort by ASCII value "A1", "A100", "A2". More...
template<typename T , typename U >
constexpr int	compare_threeway (T lhs, U rhs)
	Three-way comparison (spaceship operator) for C++ <20. More...
template<class C , class T >
bool	contains (const C &v, const T &x)
	Returns whether a container object has a certain element. More...
bool	contains_ci (std::vector< std::string > const &haystack, std::string const &needle)
	Return whether a vector of strings contains a given string, case insensitive. More...
bool	contains_ci_alnum (std::vector< std::string > const &haystack, std::string const &needle)
	Return whether a vector of strings contains a given string, case insensitive, and ignoring all non-alphanumerical characters. More...
template<class C >
bool	contains_duplicates (C const &v)
	Return whether a container contains duplicates. More...
template<typename T >
T	convert_from_string (std::string const &str, bool trim=false)
	Generic conversion from string to any data type that is supported by std::stringsteam operator >>. More...
template<>
double	convert_from_string< double > (std::string const &str, bool trim)
	Specialization of the generic conversion function for double, which also takes nan and inf into account. More...
template<>
std::string	convert_from_string< std::string > (std::string const &str, bool trim)
	Specialization of the generic conversion function for std::string. More...
GeoCoordinate	convert_geo_coordinate (std::string const &coordinate)
	Parse a string of geographic coordinates. More...
GeoCoordinate	convert_geo_coordinate (std::string const &latitude, std::string const &longitude)
	Parse strings of geographic coordinates. More...
static double	convert_single_geo_coordinate_ (std::string const &h1, std::string const &d, std::string const &m, std::string const &s, std::string const &h2, GeoCoordinateComponent component)
	Local helper function that takes parts of the regex matches and converts them to double. More...
void	convert_to_bool (Dataframe &df, size_t col_index)
void	convert_to_bool (Dataframe &df, std::string const &col_name)
template<typename ForwardIterator >
std::vector< bool >	convert_to_bool (ForwardIterator first, ForwardIterator last, size_t size=0)
bool	convert_to_bool (std::string const &str)
	Convert a string to bool, return the result, and throw an exception when the conversion was not successful. More...
bool	convert_to_bool (std::string const &str, bool &result)
	Convert a string to bool, store the result in result, and return whether the conversion as successful. More...
template<typename ForwardIterator >
std::vector< double >	convert_to_bool_double (ForwardIterator first, ForwardIterator last, size_t size=0)
double	convert_to_bool_double (std::string const &str)
	Convert a string to bool, but return it as a double, and throw an exception when the conversion was not successful. More...
bool	convert_to_bool_double (std::string const &str, double &result)
	Convert a string to bool, but store the result as a double in result, and return whether the conversion as successful. More...
void	convert_to_double (Dataframe &df, size_t col_index)
void	convert_to_double (Dataframe &df, std::string const &col_name)
template<typename ForwardIterator >
std::vector< double >	convert_to_double (ForwardIterator first, ForwardIterator last, size_t size=0)
double	convert_to_double (std::string const &str)
	Convert a string to double, return the result, and throw an exception when the conversion was not successful. More...
bool	convert_to_double (std::string const &str, double &result)
	Convert a string to double, store the result in result, and return whether the conversion as successful. More...
template<typename T , class F >
bool	convert_to_numeric_ (std::string const &str, T &result, T initial, F conversion)
static std::vector< Color >	convert_to_palette_ (NamedColorList const &list)
	Local helper function to convert a list of byte colors into a proper Color vector. More...
template<typename ForwardIterator >
std::vector< long long >	convert_to_signed_integer (ForwardIterator first, ForwardIterator last, size_t size=0)
long long	convert_to_signed_integer (std::string const &str)
	Convert a string to signed integer, return the result, and throw an exception when the conversion was not successful. More...
bool	convert_to_signed_integer (std::string const &str, long long &result)
	Convert a string to signed integer, store the result in result, and return whether the conversion as successful. More...
template<typename ForwardIterator >
std::vector< std::tm >	convert_to_tm (ForwardIterator first, ForwardIterator last, size_t size=0)
	Convert a list of std::string to std::tm date/time objects, if possible. Throw otherwise. More...
template<typename ForwardIterator >
std::vector< std::tm >	convert_to_tm (ForwardIterator first, ForwardIterator last, std::string const &format, size_t size=0)
	Convert a list of std::string to std::tm date/time objects, if possible. Throw otherwise. More...
template<typename ForwardIterator >
std::vector< std::tm >	convert_to_tm (ForwardIterator first, ForwardIterator last, std::string const &format, std::string const &locale, size_t size=0)
	Convert a list of std::string to std::tm date/time objects, if possible. Throw otherwise. More...
std::tm	convert_to_tm (std::string const &str)
	Convert a std::string to a std::tm date/time object, if possible. Throw otherwise. More...
std::tm	convert_to_tm (std::string const &str, std::string const &format)
	Convert a std::string to a std::tm date/time object, if possible. Throw otherwise. More...
std::tm	convert_to_tm (std::string const &str, std::string const &format, std::string const &locale)
	Convert a std::string to a std::tm date/time object, if possible. Throw otherwise. More...
bool	convert_to_tm_ (std::string const &str, std::string const &format, std::string const &locale, std::tm &t)
	Local helper function that does the heavy load of time conversion. More...
template<typename S , typename T >
void	convert_to_type_ (Dataframe &df, size_t col_index)
template<typename T >
void	convert_to_type_ (Dataframe &df, size_t col_index)
template<typename ForwardIterator >
std::vector< unsigned long long >	convert_to_unsigned_integer (ForwardIterator first, ForwardIterator last, size_t size=0)
unsigned long long	convert_to_unsigned_integer (std::string const &str)
	Convert a string to unsigned integer, return the result, and throw an exception when the conversion was not successful. More...
bool	convert_to_unsigned_integer (std::string const &str, unsigned long long &result)
	Convert a string to unsigned integer, store the result in result, and return whether the conversion as successful. More...
Matrix< double >	correlation_matrix (Matrix< double > const &data)
	Calculate the correlation Matrix of a given data Matrix. More...
template<class ForwardIterator >
std::pair< size_t, size_t >	count_finite_elements (ForwardIterator first, ForwardIterator last)
	Count the number of finite elements in a range of double values. More...
size_t	count_substring_occurrences (std::string const &str, std::string const &sub)
	Return the number of (possibly overlapping) occurrences of a substring in a string. More...
Matrix< double >	covariance_matrix (Matrix< double > const &data)
	Calculate the covariance Matrix of a given data Matrix. More...
constexpr double	cubed (double x)
	Cube of a number. More...
std::string	current_date ()
	Returns the current date as a string in the format "2014-12-31". More...
std::string	current_path ()
	Return the current (working) directory, simiar to getcwd(). More...
static std::string	current_path_getcwd_ ()
static std::string	current_path_unix_ ()
std::string	current_time ()
	Returns the current time as a string in the format "13:37:42". More...
char	deescape (char c)
	Return the de-escaped char for a backslash-escaped char. More...
std::string	deescape (std::string const &text)
	Return a string where backslash-escaped characters are transformed into their respective string form. More...
template<typename T >
void	descending (T &f, T &s)
	Sort two values in descending order, inplace. More...
bool	detect_OS_AVX512_ ()
bool	detect_OS_AVX_ ()
bool	detect_OS_x64_ ()
void	dir_create (std::string const &path, bool with_parents=true)
	Create a directory. More...
bool	dir_exists (std::string const &dir)
	Return true iff the directory exists. More...
std::vector< std::string >	dir_list_contents (std::string const &dir, bool full_path=false, std::string const &regex="")
	Get a list of files and directories in a directory. More...
static std::vector< std::string >	dir_list_contents_ (std::string const &dir, bool full_path, std::string const &regex, std::function< bool(std::string const &)> condition)
std::vector< std::string >	dir_list_directories (std::string const &dir, bool full_path=false, std::string const &regex="")
	Get a list of directories in a directory. More...
std::vector< std::string >	dir_list_files (std::string const &dir, bool full_path=false, std::string const &regex="")
	Get a list of files in a directory. More...
std::string	dir_normalize_path (std::string const &path)
	Normalize a dir name, i.e., make sure that the given path ends with exaclty one slash. More...
TableLayout	double_frame (bool condensed)
TableLayout	double_grid (bool condensed)
double	earth_movers_distance (const Histogram &h1, const Histogram &h2, bool norm)
bool	ends_with (std::string const &text, std::string const &suffix)
	Return whether a string ends with another string, i.e., check for a suffix. More...
bool	ends_with (std::string const &text, std::string const &suffix, std::string &prefix)
	Return whether a string ends with another string, i.e., check for a suffix. More...
bool	ends_with_ci (std::string const &text, std::string const &suffix)
	Return whether a string ends with another string, i.e., check for a suffix, case insensitive. More...
bool	ends_with_ci (std::string const &text, std::string const &suffix, std::string &prefix)
	Return whether a string ends with another string, i.e., check for a suffix, case insensitive. More...
bool	ends_with_ci_alnum (std::string const &text, std::string const &suffix)
	Return whether a string ends with another string (suffix), comparing case-independent, and ignoring all non-alphanumerical characters. More...
bool	ends_with_ci_alnum (std::string const &text, std::string const &suffix, std::string &prefix, bool trim_prefix=false)
	Return whether a string ends with another string (suffix), comparing case-independent, and ignoring all non-alphanumerical characters. More...
bool	equal_ranges (Histogram const &lhs, Histogram const &rhs)
bool	equals_ci (std::string const &lhs, std::string const &rhs)
	Compare two strings, case insensitive. More...
bool	equals_ci_alnum (std::string const &lhs, std::string const &rhs)
	Compare two strings, case insensitive, and ignoring all non-alphanumerical characters. More...
template<class Container , class UnaryPredicate >
void	erase_if (Container &c, UnaryPredicate p)
	Erases all elements from the container that satisfy a given predicate. An element is erased, if the predicate evaluates to true for it. The predicate needs to have a signature similar to (T const&)->bool. More...
std::string	escape (std::string const &text)
	Return a string where special chars are replaces by their escape sequence. More...
template<class ForwardIteratorA , class ForwardIteratorB >
double	euclidean_distance (ForwardIteratorA first_a, ForwardIteratorA last_a, ForwardIteratorB first_b, ForwardIteratorB last_b)
	Calculate the Euclidean norm (L2 norm) distance between two (mathematical) vectors. More...
double	euclidean_distance (std::vector< double > const &vec_a, std::vector< double > const &vec_b)
	Calculate the Euclidean norm (L2 norm) distance between two vectors of double elements. More...
Matrix< double >	euclidean_distance_matrix (Matrix< double > const &data)
	Calculate the pairwise euclidean distance matrix between the rows of a given matrix. More...
template<class ForwardIterator >
double	euclidean_norm (ForwardIterator first, ForwardIterator last)
	Calculate the Euclidean norm (L2 norm) of a range of numbers. More...
double	euclidean_norm (std::vector< double > const &vec)
	Calculate the Euclidean norm (L2 norm) of a std::vector of double elements. More...
TableLayout	extended_frame (bool condensed)
TableLayout	extended_grid (bool condensed)
void	file_append (std::string const &content, std::string const &filename, bool create_dirs=true)
	Append the content of a string to a file. More...
std::string	file_basename (std::string const &filename)
	Remove directory name from file name if present. More...
std::string	file_basename (std::string const &filename, std::vector< std::string > const &remove_extensions)
	Remove the directory name from a file name if present, and remove a list of given extensions. More...
bool	file_exists (std::string const &filename)
	Return true iff the file exists (and is in fact a file, and not, e.g., a directory). More...
std::string	file_extension (std::string const &filename)
	Return the extension name of a file. More...
std::string	file_filename (std::string const &filename)
	Remove extension if present. More...
std::unordered_map< std::string, std::string >	file_info (std::string const &filename)
	Return information about a file. More...
bool	file_is_readable (std::string const &filename)
	Return whether a file is readable. More...
bool	file_is_readable (std::string const &filename, std::string &err_str)
	Return whether a file is readable, and potentially store the error message. More...
void	file_output_stream (std::string const &file_name, std::ofstream &out_stream, std::ios_base::openmode mode=std::ios_base::out, bool create_dirs=true)
	Helper function to obtain an output stream to a file. More...
std::string	file_path (std::string const &filename)
	Return the path leading to a file. More...
std::string	file_read (std::string const &filename, bool detect_compression=true)
	Return the contents of a file as a string. More...
std::vector< std::string >	file_read_lines (std::string const &filename, bool detect_compression=true)
	Return the contents of a file as a vector of strings, one entry for each line. More...
size_t	file_size (std::string const &filename)
	Return the size of a file. More...
void	file_write (std::string const &content, std::string const &filename, bool create_dirs=true)
	Write the content of a string to a file. More...
std::vector< size_t >	filter_constant_columns (Matrix< double > &data, double epsilon=1e-5)
	Filter out columns that have nearly constant values, measured using an epsilon. More...
template<class ForwardIterator >
double	finite_maximum (ForwardIterator first, ForwardIterator last)
	Return the maximum of a range of double values. More...
template<class ForwardIterator >
double	finite_minimum (ForwardIterator first, ForwardIterator last)
	Return the minimum of a range of double values. More...
template<class ForwardIterator >
MinMaxPair< double >	finite_minimum_maximum (ForwardIterator first, ForwardIterator last)
	Return the minimum and the maximum of a range of double values. More...
template<class ForwardIteratorA , class ForwardIteratorB >
std::pair< std::vector< double >, std::vector< double > >	finite_pairs (ForwardIteratorA first_a, ForwardIteratorA last_a, ForwardIteratorB first_b, ForwardIteratorB last_b)
	Helper function that cleans two ranges of double of the same length from non-finite values. More...
double	fisher_transformation (double correlation_coefficient)
	Apply Fisher z-transformation to a correlation coefficient. More...
std::vector< double >	fisher_transformation (std::vector< double > const &correlation_coefficients)
	Apply Fisher z-transformation to a vector of correlation coefficients. More...
template<class ForwardIteratorA , class ForwardIteratorB >
void	for_each_finite_pair (ForwardIteratorA first_a, ForwardIteratorA last_a, ForwardIteratorB first_b, ForwardIteratorB last_b, std::function< void(double value_a, double value_b)> execute)
	Iterate two ranges of double values in parallel, and execute a function for each pair of values from the two ranges where both values are finite. More...
template<class ForwardIteratorA , class ForwardIteratorB >
double	fraction_of_variance_unexplained (ForwardIteratorA first_x, ForwardIteratorA last_x, ForwardIteratorB first_y, ForwardIteratorB last_y, LinearFunction lin_fct)
	Calculate the fraction of unexplained variance resulting from a linear fit of the input variables. More...
std::shared_ptr< BaseInputSource >	from_file (std::string const &file_name, bool detect_compression=true)
	Obtain an input source for reading from a file. More...
template<typename InputIterator >
std::vector< std::shared_ptr< BaseInputSource > >	from_files (InputIterator first, InputIterator last, bool detect_compression=true)
	Obtain a set of input sources for reading from files. More...
std::vector< std::shared_ptr< BaseInputSource > >	from_files (std::vector< std::string > const &file_names, bool detect_compression=true)
	Obtain a set of input sources for reading from files. More...
TwobitVector	from_nucleic_acids (std::string const &sequence)
	Turn a string of nucleic acids into a TwobitVector. More...
std::shared_ptr< BaseInputSource >	from_stdin ()
	Obtain an input source for reading from standard input (i.e., stdin or cin). More...
std::shared_ptr< BaseInputSource >	from_stream (std::istream &input_stream)
	Obtain an input source for reading from a stream. More...
std::shared_ptr< BaseInputSource >	from_string (std::string const &input_string)
	Obtain an input source for reading from a string. More...
template<typename InputIterator >
std::vector< std::shared_ptr< BaseInputSource > >	from_strings (InputIterator first, InputIterator last)
	Obtain a set of input sources for reading from strings. More...
std::vector< std::shared_ptr< BaseInputSource > >	from_strings (std::vector< std::string > const &input_strings)
	Obtain a set of input sources for reading from strings. More...
double	geo_distance (GeoCoordinate const &c1, GeoCoordinate const &c2)
	Calculate the distance (in km) between two points on Earth. More...
template<class ForwardIterator >
double	geometric_mean (ForwardIterator first, ForwardIterator last)
	Calculate the geometric mean of a range of positive numbers. More...
double	geometric_mean (std::vector< double > const &vec)
	Calculate the geometric mean of a std::vector of double elements. More...
static std::string	get_attribute_string_ (Style const &s)
	Internal helper function that returns the attribute string of a Style based on its properties. More...
static std::array< std::pair< std::string, std::string >, 17 >::const_iterator	get_background_color_iterator (std::string name)
	Internal helper function that returns an iterator into the background color list. More...
static NamedColorList::const_iterator	get_color_list_iterator_ (NamedColorList const &list, std::string name)
	Internal helper function. More...
size_t	get_core_id_ (std::string const &cpu_path)
std::string	get_cpu_model_ ()
void	get_cpuid_ (int32_t out[4], int32_t eax, int32_t ecx)
static std::array< std::pair< std::string, std::string >, 17 >::const_iterator	get_foreground_color_iterator (std::string name)
	Internal helper function that returns an iterator into the foreground color list. More...
size_t	get_memtotal_ ()
size_t	get_numa_node_id_ (std::string const &cpu_path)
int	get_physical_core_count_ (size_t n_cpu)
std::string	get_vendor_string_ ()
std::vector< double >	glm_coefficients (Matrix< double > const &x_predictors, std::vector< double > const &y_response, GlmLink const &link, GlmOutput const &output)
	Compute the model coefficients of a glm_fit(). More...
std::vector< double >	glm_coefficients (Matrix< double > const &x_predictors, std::vector< double > const &y_response, GlmOutput const &output)
	Compute the model coefficients of a glm_fit(). More...
Matrix< double >	glm_convert_dataframe (Dataframe const &df)
Matrix< double >	glm_convert_dataframe (Dataframe const &df, std::vector< std::string > row_order)
std::vector< double >	glm_estimate_betas (GlmOutput const &output)
	Compute the beta estimates resulting from a glm_fit(). More...
std::pair< std::vector< double >, std::vector< double > >	glm_estimate_betas_and_var_covar (GlmOutput const &output, std::vector< double > const &meat)
std::vector< double >	glm_estimate_betas_inv_tri_ (GlmOutput const &output, std::vector< double > const &inv_tri)
	Helper function to compute the betas, given that we have already inverted the tri matrix. More...
double	glm_estimate_intercept (Matrix< double > const &x_predictors, std::vector< double > const &y_response, GlmLink const &link, GlmOutput const &output, std::vector< double > const &betas)
	Compute the intercept resulting from a glm_fit(). More...
double	glm_estimate_intercept (Matrix< double > const &x_predictors, std::vector< double > const &y_response, GlmOutput const &output, std::vector< double > const &betas)
	Compute the intercept resulting from a glm_fit(). More...
template<class ForwardIterator >
GlmFactor< typename ForwardIterator::value_type >	glm_factor (ForwardIterator first, ForwardIterator last)
template<class ForwardIterator >
GlmFactor< typename ForwardIterator::value_type >	glm_factor (ForwardIterator first, ForwardIterator last, std::vector< typename ForwardIterator::value_type > const &levels)
template<class ForwardIterator >
GlmFactor< typename ForwardIterator::value_type >	glm_factor (ForwardIterator first, ForwardIterator last, std::vector< typename ForwardIterator::value_type > const &levels, std::vector< typename ForwardIterator::value_type > const &exclude)
	Reduce a list of values in the given range to a set of unique factors. More...
template<class T >
std::vector< size_t >	glm_factor_summary (GlmFactor< T > const &factor)
	Get the number of occurrences of each level in a GlmFactor. More...
GlmFamily	glm_family_binomial ()
	Binomial family functions. More...
GlmFamily	glm_family_gamma ()
	Gamma family functions. More...
GlmFamily	glm_family_gaussian ()
	Gaussian/normal family functions. More...
GlmFamily	glm_family_poisson ()
	Poisson family functions. More...
GlmOutput	glm_fit (Matrix< double > const &x_predictors, std::vector< double > const &y_response, GlmExtras const &extras={}, GlmControl const &control={})
	Fit a Generalized Linear Model (GLM) using a linear gaussian model. More...
GlmOutput	glm_fit (Matrix< double > const &x_predictors, std::vector< double > const &y_response, GlmFamily const &family, GlmExtras const &extras={}, GlmControl const &control={})
	Fit a Generalized Linear Model (GLM). More...
GlmOutput	glm_fit (Matrix< double > const &x_predictors, std::vector< double > const &y_response, GlmFamily const &family, GlmLink const &link, GlmExtras const &extras={}, GlmControl const &control={})
	Fit a Generalized Linear Model (GLM). More...
static void	glm_gaussian_ (Matrix< double > const &x_predictors, std::vector< double > const &y_response, GlmExtras const &extras, GlmControl const &control, GlmFreedom const &freedom, GlmOutput &result)
template<class T >
Dataframe	glm_indicator_variables (GlmFactor< T > const &factor, std::vector< std::string > const &row_names=std::vector< std::string >{})
	Turn a GlmFactor into a set of (dummy) indicator variables to be used in regression. More...
template<class T >
Dataframe	glm_indicator_variables (GlmFactor< T > const &factor, T const &reference_level, std::vector< std::string > const &row_names=std::vector< std::string >{})
	Turn a GlmFactor into a set of (dummy) indicator variables to be used in regression. More...
std::vector< double >	glm_inv_tri_ (std::vector< double > const &tri, size_t M)
	Invert diagonal and unit upper triangular matrices stored as one array. More...
static void	glm_irls_ (Matrix< double > const &x_predictors, std::vector< double > const &y_response, GlmFamily const &family, GlmLink const &link, GlmExtras const &extras, GlmControl const &control, GlmOutput &result)
GlmLink	glm_link_identity ()
	Identity link functions. More...
GlmLink	glm_link_inverse ()
	Inverse link functions. More...
GlmLink	glm_link_log ()
	Log link functions. More...
GlmLink	glm_link_logit ()
	Logit link functions. More...
Dataframe	glm_prepare_dataframe (Dataframe const &df)
Dataframe	glm_prepare_dataframe (Dataframe const &df, std::string &report)
Color	gradient (std::map< double, Color > const &ranges, double value)
	Returns a Color that is created using a color gradient. More...
size_t	guess_number_of_threads (bool use_openmp=true, bool use_slurm=true, bool physical_cores=true)
	Make an educated guess on the number of threads to use for multi-threaded functionality. More...
template<class ForwardIterator >
double	harmonic_mean (ForwardIterator first, ForwardIterator last, HarmonicMeanZeroPolicy zero_policy=HarmonicMeanZeroPolicy::kThrow)
	Calculate the harmonic mean of a range of positive numbers. More...
double	harmonic_mean (std::vector< double > const &vec, HarmonicMeanZeroPolicy zero_policy=HarmonicMeanZeroPolicy::kThrow)
	Calculate the harmonic mean of a std::vector of double elements. More...
template<typename T >
constexpr std::size_t	hash_combine (std::size_t seed, T const &value)
	Combine a seed value (e.g., another hash) with the hash of a given type. More...
std::string	hash_hex (std::shared_ptr< BaseInputSource > source, HashingFunctions hash_fct)
	Calculate the hash of an input source, using a given hashing function, and return its hex representation as a string. More...
std::string	head (std::string const &text, size_t lines=10)
	Return the first lines of the text. More...
Color	heat_gradient (double percentage)
	Return a Color that represents a heat gradient for a given percentage value. More...
template<class ColorNorm >
Matrix< utils::Color >	heat_map_matrix_range_ (Matrix< double > const &values, HeatmapParameters const &parameters)
template<class ColorNorm >
Matrix< utils::Color >	heat_map_matrix_range_all_ (Matrix< double > const &values, HeatmapParameters const &parameters)
template<class ColorNorm >
Matrix< utils::Color >	heat_map_matrix_range_col_ (Matrix< double > const &values, HeatmapParameters const &parameters)
template<class ColorNorm >
Matrix< utils::Color >	heat_map_matrix_range_row_ (Matrix< double > const &values, HeatmapParameters const &parameters)
MinMaxPair< double >	heat_map_matrix_update_min_max_ (MinMaxPair< double > const &min_max, HeatmapParameters const &parameters)
size_t	hypergeometric_distribution (size_t n1, size_t n2, size_t t)
	Select a random sample from a hypergeometric distribution. More...
size_t	hypergeometric_distribution_gsl (size_t n1, size_t n2, size_t t)
size_t	hypergeometric_distribution_inversion_mode_ (size_t n, size_t m, size_t N)
size_t	hypergeometric_distribution_ratio_of_unifoms_ (size_t n, size_t m, size_t N)
std::string	indent (std::string const &text, std::string const &indentation=" ")
	Indent each line of text with indentation and return the result. More...
double	index_of_dispersion (MeanStddevPair const &ms)
	Calculate the index of dispersion. More...
std::vector< double >	index_of_dispersion (std::vector< MeanStddevPair > const &ms)
	Calculate the index of dispersion. More...
InfoCompiler const &	info_get_compiler ()
	Return information about compiler settings and flags. More...
InfoHardware const &	info_get_hardware ()
	Return information about hardware features. More...
size_t	info_get_pid ()
	Get the process ID of the current process. More...
bool	info_hyperthreads_enabled ()
	Try to get whether hyperthreads are enabled in the current system. More...
size_t	info_number_of_threads_openmp ()
	Get the number of threads as indicated by the OpenMP environment. More...
size_t	info_number_of_threads_slurm ()
	Get the number of threads as indicated by the SLURM environment. More...
long	info_online_cpu_cores ()
size_t	info_physical_core_count ()
	Get the number of CPU cores. More...
std::unordered_map< std::string, std::string > const &	info_preprocessor_definitions ()
	Return a string map with some relevant preprocessor macros. More...
std::string	info_print_compiler ()
	Print information about compiler settings and flags to a string. More...
std::string	info_print_hardware (bool full=false)
	Print information about hardware features to a string. More...
double	info_process_current_cpu_usage (bool all_cores=true, bool percent=true)
	Return the CPU usage of the current process. More...
size_t	info_process_current_file_count ()
	Return the number of files (i.e., file descriptors) that the current process (the process calling this function) has opened at the moment. More...
size_t	info_process_current_memory_usage ()
	Return the memory currently used by the current process, in bytes. More...
size_t	info_process_max_file_count ()
	Return the maximum number of files (i.e., file descriptors) that can be opened simultaneously in the current process. More...
size_t	info_process_peak_memory_usage ()
	Get the peak used memory, in bytes. More...
std::string	info_process_print_total_usage ()
	Print usage information to a string. More...
std::pair< double, double >	info_process_total_cpu_time ()
	Get the currently used cpu run time, similar to the Unix time command. More...
double	info_process_total_energy_consumption ()
	Get energy consumption of the program so far, in Wh. More...
bool	info_stderr_is_terminal ()
	Return true iff the standard error stream is a terminal, and false if not, i.e., if it is a file or a pipe. More...
bool	info_stdin_is_terminal ()
	Return true iff the standard input stream is a terminal, and false if not, i.e., if it is a file or a pipe. More...
bool	info_stdout_is_terminal ()
	Return true iff the standard output stream is a terminal, and false if not, i.e., if it is a file or a pipe. More...
double	info_system_current_cpu_usage (bool all_cores=true, bool percent=true)
	Return the CPU usage of the system, across all cores. More...
size_t	info_system_current_memory_available ()
	Return the memory currently available in the system, in bytes. More...
size_t	info_system_current_memory_usage ()
	Return the memory currently used across all running processes, in bytes. More...
unsigned int	info_task_cpu_cores (bool physical=false)
std::pair< int, int >	info_terminal_size ()
	Return the width and height of the terminal that is used to run the program, in number of columns and lines. More...
bool	info_use_avx ()
	Assess if it is safe to use AVX features. More...
bool	info_use_avx2 ()
	Assess if it is safe to use AVX2 features. More...
bool	info_use_avx512 ()
	Assess if it is safe to use AVX512 features. More...
template<typename T >
std::vector< T >::iterator	insert_sorted (std::vector< T > &vec, T const &item)
	Insert into a vector vec, sorted by the value of the item. The vector must already be sorted. More...
template<typename T , typename Pred >
std::vector< T >::iterator	insert_sorted (std::vector< T > &vec, T const &item, Pred pred)
	Insert into a vector vec, sorted by the value of the item, using a predicate. The vector must already be sorted according to the predicate. More...
size_t	int_pow (size_t base, size_t exp)
	Calculate the power base^exp for positive integer values. More...
Color	interpolate (Color const &color1, Color const &color2, double fraction)
	Linearily interpolate between two Colors. More...
constexpr bool	is_alnum (char c) noexcept
	Return whether a char is a letter (a-z or A-Z) or a digit (0-9), ASCII-only. More...
constexpr bool	is_alpha (char c) noexcept
	Return whether a char is a letter (a-z or A-Z), ASCII-only. More...
constexpr bool	is_ascii (char c) noexcept
	Return whether a char is pure ASCII, that is, in the range [0, 127]. More...
template<typename T >
constexpr bool	is_ascii (std::false_type, T c) noexcept
	Implementation detail for is_ascii(char). More...
template<typename T >
constexpr bool	is_ascii (std::true_type, T c) noexcept
	Implementation detail for is_ascii(char). More...
constexpr bool	is_blank (char c) noexcept
	Return whether a char is either a space or a tab character. More...
bool	is_canonical_link (GlmFamily const &family, GlmLink const &link)
constexpr bool	is_cntrl (char c) noexcept
	Return whether a char is a control character, according to iscntrl of the cctype> heade but ASCII-only. More...
bool	is_color_name (std::string const &name)
	Return true if the name represents one of the named colors offered by genesis, which is (currently) a shortcut for is_color_name_web() and is_color_name_xkcd(). More...
bool	is_color_name_lego (std::string const &name)
	Return true iff the given name is a named LEGO color. More...
bool	is_color_name_web (std::string const &name)
	Return true iff the given name is a named web color. More...
bool	is_color_name_xkcd (std::string const &name)
	Return true iff the given name is a named xkcd color. More...
constexpr bool	is_control (char c) noexcept
	Return whether a char is a control character, excluding white spaces, ASCII-only. More...
bool	is_convertible_to_bool (Dataframe const &df, size_t col_index)
bool	is_convertible_to_bool (Dataframe const &df, std::string const &col_name)
template<typename ForwardIterator >
bool	is_convertible_to_bool (ForwardIterator first, ForwardIterator last)
bool	is_convertible_to_bool (std::string const &str)
	Return whether a string can be converted to bool. More...
template<typename ForwardIterator >
bool	is_convertible_to_bool_double (ForwardIterator first, ForwardIterator last)
bool	is_convertible_to_bool_double (std::string const &str)
	Return whether a string can be converted to bool (and stored as a double). More...
bool	is_convertible_to_double (Dataframe const &df, size_t col_index)
bool	is_convertible_to_double (Dataframe const &df, std::string const &col_name)
template<typename ForwardIterator >
bool	is_convertible_to_double (ForwardIterator first, ForwardIterator last)
bool	is_convertible_to_double (std::string const &str)
	Return whether a string can be converted to double. More...
template<typename ForwardIterator >
bool	is_convertible_to_signed_integer (ForwardIterator first, ForwardIterator last)
bool	is_convertible_to_signed_integer (std::string const &str)
	Return whether a string can be converted to signed integer. More...
template<typename ForwardIterator >
bool	is_convertible_to_tm (ForwardIterator first, ForwardIterator last)
	Return whether a list of std::string is convertible to std::tm date/time objects. More...
template<typename ForwardIterator >
bool	is_convertible_to_tm (ForwardIterator first, ForwardIterator last, std::string const &format)
	Return whether a list of std::string is convertible to std::tm date/time objects. More...
template<typename ForwardIterator >
bool	is_convertible_to_tm (ForwardIterator first, ForwardIterator last, std::string const &format, std::string const &locale)
	Return whether a list of std::string is convertible to std::tm date/time objects. More...
bool	is_convertible_to_tm (std::string const &str)
	Return whether a std::string is convertible to a std::tm date/time object, that is, whether it contains a date/time in a recognizable format. More...
bool	is_convertible_to_tm (std::string const &str, std::string const &format)
	Return whether a std::string is convertible to a std::tm date/time object, that is, whether it contains a date/time in a recognizable format. More...
bool	is_convertible_to_tm (std::string const &str, std::string const &format, std::string const &locale)
	Return whether a std::string is convertible to a std::tm date/time object, that is, whether it contains a date/time in a recognizable format. More...
template<typename ForwardIterator >
bool	is_convertible_to_unsigned_integer (ForwardIterator first, ForwardIterator last)
bool	is_convertible_to_unsigned_integer (std::string const &str)
	Return whether a string can be converted to unsigned integer. More...
bool	is_defined (GlmFamily const &family)
	Check whether all necessary values and functors of a GlmFamily are set. More...
bool	is_defined (GlmLink const &link)
	Check whether all necessary values and functors of a GlmLink are set. More...
constexpr bool	is_digit (char c) noexcept
	Return whether a char is a digit (0-9), ASCII-only. More...
bool	is_dir (std::string const &path)
	Return true iff the provided path is a directory. More...
bool	is_file (std::string const &path)
	Return true iff the provided path is a (readable) file. More...
constexpr bool	is_graph (char c) noexcept
	Return whether a char is a character with graphical representation, according to isgraph of the cctype header, but ASCII-only. More...
bool	is_gzip_compressed_file (std::string const &file_name)
	Return whether a given file is gzip-compressed. More...
constexpr bool	is_lower (char c) noexcept
	Return whether a char is a lower case letter (a-z), ASCII-only. More...
constexpr bool	is_newline (char c) noexcept
	Return whether a char is either a new line or a carriage return character. More...
static bool	is_numerical_type_ (Dataframe const &df, size_t col_index)
constexpr bool	is_other_space (char c) noexcept
	Return whether a char is some other white space charater that is neither space, tab, new line, or carriage return - that is, whether it is a form feed or a vertical tab. More...
constexpr bool	is_print (char c) noexcept
	Return whether a char is a printable character, according to isprint of the cctype header, but ASCII-only. More...
constexpr bool	is_punct (char c) noexcept
	Return whether a char is a punctuation mark, according to ispunct of the cctype header, but ASCII-only. More...
constexpr bool	is_space (char c) noexcept
	Return whether a char is some form of white space charater, so either space, tab, new line, carriage return, form feed, or vertical tab. More...
template<typename T >
bool	is_square (Matrix< T > const &data)
	Return whether a Matrix is a square matrix, that is, whether its number of rows and number of columns are idetical. More...
bool	is_strict_subset (Bitvector const &sub, Bitvector const &super)
	Strict subset. More...
bool	is_strict_superset (Bitvector const &super, Bitvector const &sub)
	Strict superset. More...
bool	is_subset (Bitvector const &sub, Bitvector const &super)
	Subset or equal. More...
bool	is_superset (Bitvector const &super, Bitvector const &sub)
	Superset or equal. More...
template<typename T >
bool	is_symmetric (Matrix< T > const &data)
	Return whether a Matrix is symmetric, i.e., whether it is square and m[ i, j ] == m[ j, i ] holds for all entries. More...
constexpr bool	is_upper (char c) noexcept
	Return whether a char is an upper case letter (A-Z), ASCII-only. More...
bool	is_valid_filename (std::string const &filename)
	Check whether a file name is valid. More...
bool	is_valid_int_pow (size_t base, size_t exp)
	Return whether the given power can be stored within a size_t. More...
constexpr bool	is_xdigit (char c) noexcept
	Return whether a char is a hexadecimal digit (0-9 or A-F or a-f), ASCII-only. More...
utils::Range< IteratorDeletions >	iterate_deletions (TwobitVector const &vector)
utils::Range< IteratorInsertions >	iterate_insertions (TwobitVector const &vector)
utils::Range< IteratorSubstitutions >	iterate_substitutions (TwobitVector const &vector)
template<typename C >
std::string	join (C const &container, std::string const &delimiter=", ")
	Return a string where the elements of a container v are joined using the string delimiter in between them. More...
template<typename DataType = EmptyIntervalData, typename NumericalType = DefaultIntervalNumericalType, typename IntervalKind = IntervalClosed>
Interval< DataType, NumericalType, IntervalKind >	join (Interval< DataType, NumericalType, IntervalKind > const &a, Interval< DataType, NumericalType, IntervalKind > const &b)
	Creates a new Interval that contains both intervals and whatever is between. More...
template<typename DataType = EmptyIntervalData, typename NumericalType = DefaultIntervalNumericalType, typename IntervalKind = IntervalClosed>
Interval< DataType, NumericalType, IntervalKind >	join (Interval< DataType, NumericalType, IntervalKind > const &a, Interval< DataType, NumericalType, IntervalKind > const &b, DataType &&data)
	Creates a new Interval that contains both intervals and whatever is between. More...
template<typename DataType = EmptyIntervalData, typename NumericalType = DefaultIntervalNumericalType, typename IntervalKind = IntervalClosed>
Interval< DataType, NumericalType, IntervalKind >	join (Interval< DataType, NumericalType, IntervalKind > const &a, Interval< DataType, NumericalType, IntervalKind > const &b, DataType const &data)
	Creates a new Interval that contains both intervals and whatever is between. More...
template<typename C , typename std::enable_if< ! std::is_same< typename C::value_type, unsigned char >::value &&! std::is_same< typename C::value_type, signed char >::value >::type * = nullptr>
std::ostream &	join (std::ostream &stream, C const &container, std::string const &delimiter=", ")
	Print elements of the given container to the output stream, joining them with the delimiter. More...
template<class InputIteratorA , class InputIteratorB >
double	kendalls_tau_correlation_coefficient (InputIteratorA first_a, InputIteratorA last_a, InputIteratorB first_b, InputIteratorB last_b, KendallsTauMethod method=KendallsTauMethod::kTauB)
double	kendalls_tau_correlation_coefficient (std::vector< double > const &x, std::vector< double > const &y, KendallsTauMethod method=KendallsTauMethod::kTauB)
	Compute Kendall's Tau Correlation Coefficient. More...
double	kendalls_tau_correlation_coefficient_clean_ (std::vector< double > const &x, std::vector< double > const &y, KendallsTauMethod method)
	Compute Kendall's Tau, expecting clean input without nan values, using Knight's algorithm. More...
double	kendalls_tau_correlation_coefficient_naive (std::vector< double > const &x, std::vector< double > const &y, KendallsTauMethod method=KendallsTauMethod::kTauB)
	Compute a simple version of Kendall's Tau Correlation Coefficient. More...
size_t	kendalls_tau_count_tau_c_m_ (std::vector< double > const &x, std::vector< double > const &y)
	Helper function to count the number of unique values in both lists, using only those entris that are finite in both. More...
template<typename T >
size_t	kendalls_tau_count_ties_ (std::vector< T > const &values)
	Helper function to count the number of tied pairs induced by equal values. More...
size_t	kendalls_tau_count_ties_sorted_ (std::vector< double > const &values)
	Helper function to count the number of tied pairs induced by equal values, on a sorted input list. More...
size_t	kendalls_tau_count_ties_sorted_pairs_rank_ (std::vector< double > const &x, std::vector< double > const &y, std::vector< size_t > const &ranks)
	Helper function to count the number of tied pairs induced by equal values, on two input list with the sorting provided via a rank indexing list. More...
size_t	kendalls_tau_count_ties_sorted_rank_ (std::vector< double > const &values, std::vector< size_t > const &ranks)
	Helper function to count the number of tied pairs induced by equal values, on a sorted input list with the sorting provided via a rank indexing list. More...
size_t	kendalls_tau_merge_count_ (std::vector< double > &data, std::vector< double > &temp, size_t left, size_t mid, size_t right)
	Helper function for kendalls_tau_correlation_coefficient() to do a merge sort that counts the number of inversions performed. More...
double	kendalls_tau_method_ (std::vector< double > const &x, std::vector< double > const &y, size_t const concordant, size_t const discordant, size_t const n, size_t const n0, size_t const n1, size_t const n2, size_t const n3, KendallsTauMethod method)
	Given counts of concordant and discordant pairs, compute the final value, applying the requested adjustments. More...
size_t	kendalls_tau_sort_and_count_ (std::vector< double > &data, std::vector< double > &temp, size_t left, size_t right)
	Helper function for kendalls_tau_correlation_coefficient() to sort a list using merge sort, while counting the number of inversions performed. More...
double	log_binomial_coefficient (size_t n, size_t k)
	Compute the logarithm (base e) of the binomial coefficient, that is n choose k, for two integer numbers, for large numbers. More...
double	log_binomial_distribution (size_t k, size_t n, double p)
	Compute the logarithm (base e) of the probability mass function for a binomial distribution. More...
double	log_factorial (size_t n)
	Return the logarithm (base e) of the factorial of n, that is log(n!). More...
std::vector< double >	log_factorial_lookup_generator_ ()
	Helper function to generate above lookup table. More...
long	logging_progress_value (long value=-1)
	Hack function to make sure that the value arugment in LOG_PROG is only evaluated once. More...
std::vector< bool >	make_bool_vector_from_indices (std::vector< size_t > const &indices, size_t size=0)
	Helper function to create a bool vector from a set of indices to be set to true. More...
template<typename PredicateFunctor , typename BaseIterator >
FilterIterator< PredicateFunctor, BaseIterator >	make_filter_iterator (PredicateFunctor unary_func, BaseIterator begin, BaseIterator end=BaseIterator{})
	Construct a filtering iterator, given the filter predicate function as well as the underlying base iterator begin and end. More...
template<typename PredicateFunctor , typename BaseIterator >
Range< FilterIterator< PredicateFunctor, BaseIterator > >	make_filter_range (PredicateFunctor unary_func, BaseIterator begin, BaseIterator end)
	Construct a filtering range, given the filter predicate function as well as the underlying base iterator begin and end. More...
template<typename PredicateFunctor , typename Container >
Range< FilterIterator< PredicateFunctor, typename Container::iterator > >	make_filter_range (PredicateFunctor unary_func, Container &container)
	Construct a filtering range, given the filter predicate function as well as a container, whose begin() and end() iterators are used, respectively. More...
template<typename PredicateFunctor , typename Container >
Range< FilterIterator< PredicateFunctor, typename Container::const_iterator > >	make_filter_range (PredicateFunctor unary_func, Container const &container)
	Construct a filtering range, given the filter predicate function as well as a const container, whose begin() and end() iterators are used, respectively. More...
std::unique_ptr< ColorNormalization >	make_heatmap_color_norm (Matrix< double > const &values, HeatmapParameters const &parameters)
Matrix< Color >	make_heatmap_matrix (Matrix< double > const &values, HeatmapParameters const &parameters)
template<typename T >
Optional< T >	make_optional (T const &v)
	Convenience function to create an Optional. More...
template<typename DataType = EmptyIntervalData, typename NumericalType = DefaultIntervalNumericalType, typename IntervalKind = IntervalClosed>
Interval< DataType, NumericalType, IntervalKind >	make_safe_interval (NumericalType lhs, NumericalType rhs)
template<typename DataType = EmptyIntervalData, typename NumericalType = DefaultIntervalNumericalType, typename IntervalKind = IntervalClosed>
Interval< DataType, NumericalType, IntervalKind >	make_safe_interval (NumericalType lhs, NumericalType rhs, DataType &&data)
template<typename DataType = EmptyIntervalData, typename NumericalType = DefaultIntervalNumericalType, typename IntervalKind = IntervalClosed>
Interval< DataType, NumericalType, IntervalKind >	make_safe_interval (NumericalType lhs, NumericalType rhs, DataType const &data)
SvgGroup	make_svg_axis (SvgAxisSettings const &settings, std::map< double, std::string > const &labels, std::string const &name="")
	Simple helper to make an axis. More...
SvgGroup	make_svg_axis (SvgAxisSettings const &settings, std::vector< Tickmarks::LabeledTick > const &labels, std::string const &name="", bool round_labels=true)
	Simple helper to make an axis. More...
std::pair< SvgGradientLinear, SvgGroup >	make_svg_color_bar (SvgColorBarSettings const &settings, ColorMap const &map, ColorNormalization const &norm, std::string const &id)
static std::pair< SvgGradientLinear, SvgGroup >	make_svg_color_bar_discrete_ (SvgColorBarSettings const &settings, std::map< double, Color > const &stops)
static std::pair< SvgGradientLinear, SvgGroup >	make_svg_color_bar_gradient_ (SvgColorBarSettings const &settings, ColorMap const &map, ColorNormalization const &norm, std::string const &id)
static void	make_svg_color_bar_tickmarks_ (SvgColorBarSettings const &settings, ColorMap const &map, ColorNormalization const &norm, SvgGroup &group)
SvgGroup	make_svg_color_list (ColorMap const &map, std::vector< std::string > const &labels)
SvgGroup	make_svg_color_list (std::vector< Color > const &colors, std::vector< std::string > const &labels)
void	make_svg_color_list_entry_ (size_t i, Color const &color, std::string const &label, SvgGroup &group)
SvgGroup	make_svg_matrix (Matrix< Color > const &mat, SvgMatrixSettings settings)
SvgGroup	make_svg_matrix (Matrix< Color > const &mat, SvgMatrixSettings settings, std::vector< std::string > const &row_labels)
SvgGroup	make_svg_matrix (Matrix< Color > const &mat, SvgMatrixSettings settings, std::vector< std::string > const &row_labels, std::vector< std::string > const &col_labels)
SvgGroup	make_svg_pie_chart (std::vector< double > const &values, std::vector< Color > const &colors, double radius=1.0, double start_angle=- PI/2.0, bool clockwise=true)
	Make a pie chart in SVG. More...
template<typename TransformFunctor , typename BaseIterator >
TransformIterator< TransformFunctor, BaseIterator >	make_transform_iterator (TransformFunctor unary_func, BaseIterator iterator)
	Construct a transforming iterator, given the underlying base iterator and the transformation function. More...
template<typename TransformFunctor , typename BaseIterator >
Range< TransformIterator< TransformFunctor, BaseIterator > >	make_transform_range (TransformFunctor unary_func, BaseIterator begin, BaseIterator end)
	Construct a transforming range, given the transformation function as well as the underlying base iterator begin and end. More...
template<typename TransformFunctor , typename Container >
Range< TransformIterator< TransformFunctor, typename Container::iterator > >	make_transform_range (TransformFunctor unary_func, Container &container)
	Construct a transforming range, given the transformation function as well as a container, whose begin() and end() iterators are used, respectively. More...
template<typename TransformFunctor , typename Container >
Range< TransformIterator< TransformFunctor, typename Container::const_iterator > >	make_transform_range (TransformFunctor unary_func, Container const &container)
	Construct a transforming range, given the transformation function as well as a const container, whose begin() and end() iterators are used, respectively. More...
template<typename T , typename... Args>
std::unique_ptr< T >	make_unique (Args &&... args)
	Returns a std::unique_ptr for a given type. More...
template<class ForwardIteratorA , class ForwardIteratorB >
double	manhattan_distance (ForwardIteratorA first_a, ForwardIteratorA last_a, ForwardIteratorB first_b, ForwardIteratorB last_b)
	Calculate the Manhattan norm (L1 norm) distance between two (mathematical) vectors. More...
double	manhattan_distance (std::vector< double > const &vec_a, std::vector< double > const &vec_b)
	Calculate the Manhattan norm (L1 norm) distance between two vectors of double elements. More...
Matrix< double >	manhattan_distance_matrix (Matrix< double > const &data)
	Calculate the pairwise manhatten distance matrix between the rows of a given matrix. More...
template<class ForwardIterator >
double	manhattan_norm (ForwardIterator first, ForwardIterator last)
	Calculate the Manhattan norm (L1 norm) of a range of numbers. More...
double	manhattan_norm (std::vector< double > const &vec)
	Calculate the Manhattan norm (L1 norm) of a std::vector of double elements. More...
bool	match_wildcards (std::string const &str, std::string const &pattern)
	Return whether a string is matched by a wildcard pattern containing ? and * for single and mutliple (0 or more) wildcard characters, respectively. More...
template<typename T = double, typename A = double, typename B = double>
Matrix< T >	matrix_addition (Matrix< A > const &a, Matrix< B > const &b)
	Calculate the element-wise sum of two Matrices. More...
template<typename T = double, typename A = double, typename B = double>
Matrix< T >	matrix_addition (Matrix< A > const &matrix, B const &scalar)
	Calculate the element-wise sum of a Matrix and a scalar. More...
template<typename T >
std::vector< MinMaxPair< T > >	matrix_col_minmax (Matrix< T > const &data, bool ignore_non_finite_values=true)
	Calculate the column-wise min and max values of a Matrix. More...
template<typename T >
std::vector< T >	matrix_col_sums (Matrix< T > const &data, bool ignore_non_finite_values=true)
	Calculate the sum of each column and return the result as a vector. More...
template<typename T >
MinMaxPair< T >	matrix_minmax (Matrix< T > const &data, bool ignore_non_finite_values=true)
	Calculate the min and max values of a Matrix. More...
template<typename T = double, typename A = double, typename B = double>
Matrix< T >	matrix_multiplication (Matrix< A > const &a, Matrix< B > const &b)
	Calculate the product of two Matrices. More...
template<typename T = double, typename A = double, typename B = double>
std::vector< T >	matrix_multiplication (Matrix< A > const &a, std::vector< B > const &b)
	Calculate the product of a Matrices a with a vector b, as if the vector was a Matrix with only one column. More...
template<typename T = double, typename A = double, typename B = double>
Matrix< T >	matrix_multiplication (Matrix< A > const &matrix, B const &scalar)
	Calculate the element-wise multiplication of a Matrix and a scalar. More...
template<typename T = double, typename A = double, typename B = double>
std::vector< T >	matrix_multiplication (std::vector< A > const &a, Matrix< B > const &b)
	Calculate the product of a vector a with a Matrices b, as if the vector was a Matrix with only one row. More...
template<typename T >
std::vector< MinMaxPair< T > >	matrix_row_minmax (Matrix< T > const &data, bool ignore_non_finite_values=true)
	Calculate the row-wise min and max values of a Matrix. More...
template<typename T >
std::vector< T >	matrix_row_sums (Matrix< T > const &data, bool ignore_non_finite_values=true)
	Calculate the sum of each row and return the result as a vector. More...
template<typename T >
Matrix< T >	matrix_sort_by_col_sum_symmetric (Matrix< T > const &data)
	Sort rows and columns of a Matrix by the sum or the columns. More...
template<typename T >
Matrix< T >	matrix_sort_by_row_sum_symmetric (Matrix< T > const &data)
	Sort rows and columns of a Matrix by the sum or the rows. More...
template<typename T >
Matrix< T >	matrix_sort_diagonal_symmetric (Matrix< T > const &data)
	Sort a Matrix so that the highest entries are on the diagonal. More...
template<typename T = double, typename A = double, typename B = double>
Matrix< T >	matrix_subtraction (Matrix< A > const &a, Matrix< B > const &b)
	Calculate the element-wise difference of two Matrices. More...
template<typename T >
T	matrix_sum (Matrix< T > const &data, bool ignore_non_finite_values=true)
	Calculate the sum of all elements in a Matrix. More...
size_t	max_bin (const Histogram &h)
double	max_value (const Histogram &h)
template<class ForwardIteratorA , class ForwardIteratorB >
double	maximum_distance (ForwardIteratorA first_a, ForwardIteratorA last_a, ForwardIteratorB first_b, ForwardIteratorB last_b)
	Calculate the Maximum norm (infinity norm) distance between two (mathematical) vectors. More...
double	maximum_distance (std::vector< double > const &vec_a, std::vector< double > const &vec_b)
	Calculate the Maximum norm (infinity norm) distance between two vectors of double elements. More...
Matrix< double >	maximum_distance_matrix (Matrix< double > const &data)
	Calculate the pairwise maximum distance matrix between the rows of a given matrix. More...
template<class ForwardIterator >
double	maximum_norm (ForwardIterator first, ForwardIterator last)
	Calculate the Maximum norm (infinity norm) of a range of numbers. More...
double	maximum_norm (std::vector< double > const &vec)
	Calculate the Maximum norm (infinity norm) of a std::vector of double elements. More...
double	mean (const Histogram &h)
	Compute the bin-weighted arithmetic mean. More...
template<class ForwardIteratorA , class ForwardIteratorB >
double	mean_squared_error (ForwardIteratorA first_x, ForwardIteratorA last_x, ForwardIteratorB first_y, ForwardIteratorB last_y, LinearFunction lin_fct)
	Calculate the mean squared error obtained from a linear fit of the input variables. More...
template<class ForwardIterator >
MeanStddevPair	mean_stddev (ForwardIterator first, ForwardIterator last, double epsilon=-1.0)
	Calculate the arithmetic mean and standard deviation of a range of double elements. More...
MeanStddevPair	mean_stddev (std::vector< double > const &vec, double epsilon=-1.0)
	Calculate the mean and standard deviation of a std::vector of double elements. More...
double	median (const Histogram &h)
template<class RandomAccessIterator >
double	median (RandomAccessIterator first, RandomAccessIterator last)
	Calculate the median value of a sorted range of double values. More...
double	median (std::vector< double > const &vec)
	Calculate the median value of a vector of double. More...
size_t	min_bin (const Histogram &h)
double	min_value (const Histogram &h)
TableLayout	minimal_layout ()
template<class T >
std::pair< T, T >	minmax_value (T const &a, T const &b)
	Returns the lowest and the greatest of the given values, by value. More...
template<class T , class Compare >
std::pair< T, T >	minmax_value (T const &a, T const &b, Compare comp)
	Returns the lowest and the greatest of the given values, by value. More...
static std::string	mode_to_string_ (std::ios_base::openmode mode)
Matrix< double >	multi_dimensional_scaling (Matrix< double > const &distances, Matrix< double > const &initial_values, size_t dimensions=2, size_t iterations=100, MdsAlgorithm algorithm=MdsAlgorithm::kUcf)
	Multi-Dimensional Scaling (MDS). More...
Matrix< double >	multi_dimensional_scaling (Matrix< double > const &distances, size_t dimensions=2, size_t iterations=100, MdsAlgorithm algorithm=MdsAlgorithm::kUcf)
	Multi-Dimensional Scaling (MDS). More...
static Matrix< double >	multi_dimensional_scaling_smacof (Matrix< double > const &distances, Matrix< double > const &initial_values, size_t dimensions, size_t iterations)
static Matrix< double >	multi_dimensional_scaling_ucf (Matrix< double > const &distances, Matrix< double > const &initial_values, size_t dimensions, size_t iterations)
std::vector< size_t >	multinomial_distribution (std::vector< double > const &p, size_t n)
	Select a random sample following a multinomial distribution. More...
std::vector< size_t >	multinomial_distribution (std::vector< size_t > const &p, size_t n)
	Select a random sample following a multinomial distribution. More...
template<class T >
std::vector< size_t >	multinomial_distribution_ (std::vector< T > const &p, size_t n)
std::vector< size_t >	multivariate_hypergeometric_distribution (std::vector< size_t > const &p, size_t n)
	Select a random sample following a multivariate hypergeometric distribution. More...
template<typename ForwardIterator , typename T = typename ForwardIterator::value_type, typename Comp = std::less<T>>
std::vector< T >	n_first_elements (ForwardIterator first, ForwardIterator last, size_t n, Comp comp=std::less< T >{})
	Return the n first elements of a given input range in sorting order. More...
void	normalize (Histogram &h, double total)
std::vector< MinMaxPair< double > >	normalize_cols (Matrix< double > &data)
	Normalize the columns of a Matrix so that all values are in the range [ 0.0, 1.0 ]. More...
std::vector< MinMaxPair< double > >	normalize_rows (Matrix< double > &data)
	Normalize the rows of a Matrix so that all values are in the range [ 0.0, 1.0 ]. More...
void	offset (Histogram &h, double value)
bool	operator!= (Color const &lhs, Color const &rhs)
bool	operator!= (JsonDocument const &lhs, JsonDocument const &rhs)
bool	operator!= (JsonDocument const &v, std::nullptr_t)
bool	operator!= (NexusTaxa const &lhs, NexusTaxa const &rhs)
template<typename T >
bool	operator!= (nullopt_t, Optional< T > const &x)
template<typename T >
bool	operator!= (Optional< T > const &x, nullopt_t)
template<typename T , typename U >
bool	operator!= (Optional< T > const &x, Optional< U > const &y)
template<typename T , typename U >
bool	operator!= (Optional< T > const &x, U const &v)
bool	operator!= (std::nullptr_t, JsonDocument const &v)
template<typename T , typename U >
bool	operator!= (U const &v, Optional< T > const &x)
Bitvector	operator& (Bitvector const &lhs, Bitvector const &rhs)
constexpr bool	operator& (SkipWhitespace lhs, SkipWhitespace rhs) noexcept
	And-operator to check whether a SkipWhitespace is set. More...
bool	operator< (const JsonDocument::ValueType lhs, const JsonDocument::ValueType rhs)
bool	operator< (JsonDocument const &lhs, JsonDocument const &rhs)
bool	operator< (JsonDocument::const_reference lhs, JsonDocument::const_reference rhs)
template<typename T >
bool	operator< (nullopt_t, Optional< T > const &x)
template<typename T >
bool	operator< (Optional< T > const &, nullopt_t)
template<typename T , typename U >
bool	operator< (Optional< T > const &x, Optional< U > const &y)
template<typename T , typename U >
bool	operator< (Optional< T > const &x, U const &v)
template<typename T , typename U >
bool	operator< (U const &v, Optional< T > const &x)
std::ostream &	operator<< (std::ostream &os, Color const &h)
	Write a textual representation of the Color the a stream, in the format "(r, g, b, a)". More...
std::ostream &	operator<< (std::ostream &os, const Histogram &h)
std::ostream &	operator<< (std::ostream &os, const HistogramAccumulator &h)
template<>
std::ostream &	operator<< (std::ostream &os, const Matrix< signed char > &matrix)
	Template specialization for signed char, in order to print nicely. More...
template<typename T >
std::ostream &	operator<< (std::ostream &os, const Matrix< T > &matrix)
	Print the elements of a Matrix to a stream, using operator << for each element. More...
template<>
std::ostream &	operator<< (std::ostream &os, const Matrix< unsigned char > &matrix)
	Template specialization for unsigned char, in order to print nicely. More...
std::ostream &	operator<< (std::ostream &os, GeoCoordinate const &coord)
std::ostream &	operator<< (std::ostream &os, NexusBlock const &block)
std::ostream &	operator<< (std::ostream &out, Bitvector const &bv)
	Insertion operator that outputs a Bitvector as a string of '0's and '1's. More...
std::ostream &	operator<< (std::ostream &out, Style const &style)
	Print the properties of a Style object to a stream. More...
std::ostream &	operator<< (std::ostream &out, Table const &table)
std::ostream &	operator<< (std::ostream &out, TableLayout::Binder const &binder)
bool	operator<= (JsonDocument const &lhs, JsonDocument const &rhs)
template<typename T >
bool	operator<= (nullopt_t, Optional< T > const &)
template<typename T >
bool	operator<= (Optional< T > const &x, nullopt_t)
template<typename T , typename U >
bool	operator<= (Optional< T > const &x, Optional< U > const &y)
template<typename T , typename U >
bool	operator<= (Optional< T > const &x, U const &v)
template<typename T , typename U >
bool	operator<= (U const &v, Optional< T > const &x)
bool	operator== (Color const &lhs, Color const &rhs)
bool	operator== (JsonDocument const &lhs, JsonDocument const &rhs)
bool	operator== (JsonDocument const &v, std::nullptr_t)
bool	operator== (JsonDocument::const_reference lhs, JsonDocument::const_reference rhs)
bool	operator== (NexusTaxa const &lhs, NexusTaxa const &rhs)
template<typename T >
bool	operator== (nullopt_t, Optional< T > const &x)
template<typename T >
bool	operator== (Optional< T > const &x, nullopt_t)
template<typename T , typename U >
bool	operator== (Optional< T > const &x, Optional< U > const &y)
template<typename T , typename U >
bool	operator== (Optional< T > const &x, U const &v)
bool	operator== (std::nullptr_t, JsonDocument const &v)
template<typename T , typename U >
bool	operator== (U const &v, Optional< T > const &x)
bool	operator> (JsonDocument const &lhs, JsonDocument const &rhs)
template<typename T >
bool	operator> (nullopt_t, Optional< T > const &)
template<typename T >
bool	operator> (Optional< T > const &x, nullopt_t)
template<typename T , typename U >
bool	operator> (Optional< T > const &x, Optional< U > const &y)
template<typename T , typename U >
bool	operator> (Optional< T > const &x, U const &v)
template<typename T , typename U >
bool	operator> (U const &v, Optional< T > const &x)
bool	operator>= (JsonDocument const &lhs, JsonDocument const &rhs)
template<typename T >
bool	operator>= (nullopt_t, Optional< T > const &x)
template<typename T >
bool	operator>= (Optional< T > const &, nullopt_t)
template<typename T , typename U >
bool	operator>= (Optional< T > const &x, Optional< U > const &y)
template<typename T , typename U >
bool	operator>= (Optional< T > const &x, U const &v)
template<typename T , typename U >
bool	operator>= (U const &v, Optional< T > const &x)
std::istream &	operator>> (std::istream &in, Bitvector &bv)
	Extraction operator that inputs a Bitvector from a string of '0's and '1's, and stops at the first char that is not '0' or '1'. More...
Bitvector	operator^ (Bitvector const &lhs, Bitvector const &rhs)
Bitvector	operator| (Bitvector const &lhs, Bitvector const &rhs)
template<class ForwardIterator >
double	p_norm (ForwardIterator first, ForwardIterator last, double p=2.0)
	Calculate the p-norm of a range of numbers. More...
double	p_norm (std::vector< double > const &vec, double p=2.0)
	Calculate the p-norm of a std::vector of double elements. More...
template<class ForwardIteratorA , class ForwardIteratorB >
double	p_norm_distance (ForwardIteratorA first_a, ForwardIteratorA last_a, ForwardIteratorB first_b, ForwardIteratorB last_b, double p=2.0)
	Calculate the p-norm distance between two (mathematical) vectors. More...
double	p_norm_distance (std::vector< double > const &vec_a, std::vector< double > const &vec_b, double p=2.0)
	Calculate the p-norm distance between two vectors of double elements. More...
Matrix< double >	p_norm_distance_matrix (Matrix< double > const &data, double p=2.0)
	Calculate the pairwise distance matrix between the rows of a given matrix. More...
template<typename F , typename T1 , typename T2 , typename T = typename std::common_type<T1, T2>::type, typename R = typename std::result_of<typename std::decay<F>::type(T, T)>::type>
MultiFuture< R >	parallel_block (T1 begin, T2 end, F &&body, std::shared_ptr< ThreadPool > thread_pool=nullptr, size_t num_blocks=0, bool auto_wait=true)
	Parallel block over a range of elements, breaking the range into blocks for which the body function is executed individually. More...
template<typename F , typename T1 , typename T2 , typename T = typename std::common_type<T1, T2>::type>
MultiFuture< void >	parallel_for (T1 begin, T2 end, F &&body, std::shared_ptr< ThreadPool > thread_pool=nullptr, size_t num_blocks=0, bool auto_wait=true)
	Parallel for over a range of positions, breaking the range into blocks for which the body function is executed individually. More...
template<typename F , typename T >
MultiFuture< void >	parallel_for_each (T &container, F &&body, std::shared_ptr< ThreadPool > thread_pool=nullptr, size_t num_blocks=0, bool auto_wait=true)
	Parallel for each over a container, processing it in blocks for which the body function is executed individually. More...
template<typename F , typename T >
MultiFuture< void >	parallel_for_each (T const begin, T const end, F &&body, std::shared_ptr< ThreadPool > thread_pool=nullptr, size_t num_blocks=0, bool auto_wait=true)
	Parallel for each over a container, processing it in blocks for which the body function is executed individually. More...
template<class T >
T	parse_float (utils::InputStream &source)
	Read a floating point number from a stream and return it. More...
template<class T >
T	parse_integer (utils::InputStream &source)
	Alias for parse_signed_integer(). More...
std::string	parse_number_string (utils::InputStream &source)
	Read a general number string from an input stream. More...
std::string	parse_quoted_string (utils::InputStream &source, bool use_escapes=true, bool use_twin_quotes=false, bool include_qmarks=false)
	Read a string in quotation marks from a stream and return it. More...
template<class T >
T	parse_signed_integer (utils::InputStream &source)
	Read a signed integer from a stream and return it. More...
template<class T >
T	parse_unsigned_integer (utils::InputStream &source)
	Read an unsigned integer from a stream and return it. More...
size_t	parse_unsigned_integer_naive_ (utils::InputStream &source)
	Naive parsing that simply loops over chars. More...
size_t	parse_unsigned_integer_size_t (utils::InputStream &source)
	Parse the input source as an unsigned int into a size_t. More...
bool	path_exists (std::string const &path)
	Return whether a path exists, i.e., is a file or directory. More...
static uint32_t	pcg32_rotr32 (uint32_t x, unsigned int r)
template<class ForwardIteratorA , class ForwardIteratorB >
double	pearson_correlation_coefficient (ForwardIteratorA first_a, ForwardIteratorA last_a, ForwardIteratorB first_b, ForwardIteratorB last_b)
	Calculate the Pearson Correlation Coefficient between two ranges of double. More...
double	pearson_correlation_coefficient (std::vector< double > const &vec_a, std::vector< double > const &vec_b)
	Calculate the Pearson Correlation Coefficient between the entries of two vectors. More...
uint32_t	permuted_congruential_generator ()
	Fast random number generator for 32bit integers. More...
uint32_t	permuted_congruential_generator (uint32_t max)
	Fast random number generator for 32bit integers, for numbers in the range [0, max]. More...
uint32_t	permuted_congruential_generator (uint32_t min, uint32_t max)
	Fast random number generator for 32bit integers, for numbers in the range [min, max]. More...
bool	permuted_congruential_generator_bool ()
	Fast random number generator for 32bit integers, for bool with 0.5 probability. More...
bool	permuted_congruential_generator_bool (uint32_t chance_one_in)
	Fast random number generator for 32bit integers, for bool with a given chance. More...
void	permuted_congruential_generator_init (uint64_t seed)
	Set the seed for permuted_congruential_generator(). More...
PcaData	principal_component_analysis (Matrix< double > const &data, size_t components=0, PcaStandardization standardization=PcaStandardization::kCorrelation)
	Perfom a Principal Component Analysis on a given data Matrix. More...
template<typename T >
std::string	print (Matrix< T > const &matrix, size_t rows=10, size_t cols=10)
	Print a Matrix to a std::string. More...
template<typename T >
void	print (std::ostream &out, Matrix< T > const &matrix, size_t rows=10, size_t cols=10)
	Print a Matrix to an out stream. See print( Matrix<T> const&, size_t, size_t ) for details. More...
template<typename T >
void	print_byte_matrix_ (std::ostream &os, const Matrix< T > &matrix, size_t width)
	Local helper function to avoid code duplication. More...
double	quartile_coefficient_of_dispersion (Quartiles const &q)
	Calculate the quartile_coefficient_of_dispersion. More...
std::vector< double >	quartile_coefficient_of_dispersion (std::vector< Quartiles > const &q)
	Calculate the quartile_coefficient_of_dispersion. More...
template<class RandomAccessIterator >
Quartiles	quartiles (RandomAccessIterator first, RandomAccessIterator last)
	Calculate the Quartiles of a sorted range of double values. More...
Quartiles	quartiles (std::vector< double > const &vec)
	Calculate the Quartiles of a vector of double. More...
template<class RandomAccessIterator >
std::vector< size_t >	ranking_dense (RandomAccessIterator first, RandomAccessIterator last)
	Return the ranking of the values in the given range, using Dense ranking ("1223" ranking). More...
std::vector< size_t >	ranking_dense (std::vector< double > const &vec)
	Return the ranking of the values in the given range, using Dense ranking ("1223" ranking). More...
template<class RandomAccessIterator >
std::vector< double >	ranking_fractional (RandomAccessIterator first, RandomAccessIterator last)
	Return the ranking of the values in the given range, using Fractional ranking ("1 2.5 2.5 4" ranking). More...
std::vector< double >	ranking_fractional (std::vector< double > const &vec)
	Return the ranking of the values in the given range, using Fractional ranking ("1 2.5 2.5 4" ranking). More...
template<class RandomAccessIterator >
std::vector< size_t >	ranking_modified (RandomAccessIterator first, RandomAccessIterator last)
	Return the ranking of the values in the given range, using Modified competition ranking ("1334" ranking). More...
std::vector< size_t >	ranking_modified (std::vector< double > const &vec)
	Return the ranking of the values in the given range, using Modified competition ranking ("1334" ranking). More...
template<class RandomAccessIterator >
std::vector< size_t >	ranking_ordinal (RandomAccessIterator first, RandomAccessIterator last)
	Return the ranking of the values in the given range, using Ordinal ranking ("1234" ranking). More...
std::vector< size_t >	ranking_ordinal (std::vector< double > const &vec)
	Return the ranking of the values in the given range, using Ordinal ranking ("1234" ranking). More...
template<class RandomAccessIterator >
std::vector< size_t >	ranking_standard (RandomAccessIterator first, RandomAccessIterator last)
	Return the ranking of the values in the given range, using Standard competition ranking ("1224" ranking). More...
std::vector< size_t >	ranking_standard (std::vector< double > const &vec)
	Return the ranking of the values in the given range, using Standard competition ranking ("1224" ranking). More...
template<typename InputStream >
char	read_char_or_throw (InputStream &source, char criterion, SkipWhitespace skip_ws=SkipWhitespace::kNone)
	Lexing function that reads a single char from the stream and checks whether it equals the provided one. More...
template<typename InputStream >
char	read_char_or_throw (InputStream &source, std::function< bool(char)> criterion, SkipWhitespace skip_ws=SkipWhitespace::kNone)
	Lexing function that reads a single char from the stream and checks whether it fulfills the provided criterion. More...
size_t	read_id_from_file_ (std::string const &filename)
template<typename InputStream >
std::string	read_to_end_of_line (InputStream &source)
	Lexing function that reads until the end of the line (i.e., to the new line char), and returns the read chars (excluding the new line char). More...
template<typename InputStream >
std::string	read_until (InputStream &source, char criterion)
	Lexing function that reads from the stream until its current char equals the provided one. The read chars are returned. More...
template<typename InputStream >
std::string	read_until (InputStream &source, std::function< bool(char)> criterion)
	Lexing function that reads from the stream until its current char fulfills the provided criterion. The read chars are returned. More...
template<typename InputStream >
std::string	read_while (InputStream &source, char criterion)
	Lexing function that reads from the stream while its current char equals the provided one. The read chars are returned. More...
template<typename InputStream >
std::string	read_while (InputStream &source, std::function< bool(char)> criterion)
	Lexing function that reads from the stream while its current char fulfills the provided criterion. The read chars are returned. More...
static bool	readlink_internal_ (const std::string &path, std::string &buffer, ssize_t length)
std::string	real_path (std::string const &path, bool resolve_link=true)
	Return the real path of a file or directory, similar to realpath(). More...
static std::string	real_path_realpath_ (std::string const &path, bool resolve_link)
static std::string	real_path_unix_ (std::string const &path, bool resolve_link)
static std::string	realpath_file_ (const std::string &path)
TridiagonalDecompositionData	reduce_to_tridiagonal_matrix (Matrix< double > &data)
	Triangular decomposition of a symmetric matrix. More...
static void	relative_dir_base_split_ (std::string const &path, std::string &dir, std::string &base)
std::string	remove_all (std::string const &text, std::string const &search)
	Return a copy of a string, where all occurrences of a search string are removed. More...
std::string	remove_all_chars (std::string const &text, std::string const &search_chars)
	Remove all occurrences of the search_chars in text. More...
template<class UnaryPredicate >
std::string	remove_all_chars_pred (std::string const &text, UnaryPredicate predicate)
	Remove all occurrences characters for which predicate is true in text. More...
std::string	remove_all_non_alnum (std::string const &text)
	Remove all non-alphanumerical characters from a string. More...
std::string	repeat (std::string const &word, size_t times)
	Take a string and repeat it a given number of times. More...
std::string	replace_all (std::string const &text, std::string const &search, std::string const &replace)
	Return a copy of a string, where all occurrences of a search string are replaced by a replace string. More...
std::string	replace_all_chars (std::string const &text, std::string const &search_chars, char replace)
	Replace all occurrences of the search_chars in text by the replace char. More...
template<class UnaryPredicate >
std::string	replace_all_chars_pred (std::string const &text, UnaryPredicate predicate, char replace)
	Replace all occurrences of characters for which predicate is true in text by the replace char. More...
Color	resolve_color_string (std::string const &color_str)
	Resolve a string representing a color. More...
double	round_to (double x, size_t accuracy_order)
	Retun the value of x, rounded to the decimal digit given by accuracy_order. More...
std::string	sanitize_filename (std::string const &filename)
	Remove or replace all invalid parts of a filename. More...
std::string	sanitize_geo_coordinate (std::string const &coordinate, bool two_components=true)
	Replace non-ascii symbols used in geographic coordinates by their ascii equivalents. More...
void	scale (Histogram &h, double factor)
std::vector< size_t >	select_without_replacement (size_t k, size_t n)
	Select k many unique numbers out of the range [ 0, n ). More...
Bitvector	set_minus (Bitvector const &lhs, Bitvector const &rhs)
double	sigma (const Histogram &h)
	Compute the bin-weighted standard deviation. More...
template<typename T >
constexpr int	signum (T x)
	Get the sign of a value, which is either -1, 0, or 1. More...
template<typename T >
constexpr int	signum (T x, std::false_type)
	Implementation of signum(T x) for unsigned types. See there for details. More...
template<typename T >
constexpr int	signum (T x, std::true_type)
	Implementation of signum(T x) for signed types. See there for details. More...
TableLayout	simple_frame (bool condensed)
TableLayout	simple_grid (bool condensed)
TableLayout	simple_layout (bool condensed)
template<class ForwardIteratorA , class ForwardIteratorB >
LinearFunction	simple_linear_regression (ForwardIteratorA first_x, ForwardIteratorA last_x, ForwardIteratorB first_y, ForwardIteratorB last_y)
	Simple linear regression, for predicting the dependent variable y given the independent variable x, using ordinary least squares regression. More...
template<typename InputStream >
void	skip_to_end_of_line (InputStream &source)
	Lexing function that advances the stream to the end of the line, i.e., to the new line char. More...
template<typename InputStream >
void	skip_until (InputStream &source, char criterion)
	Lexing function that advances the stream until its current char equals the provided one. More...
template<typename InputStream >
void	skip_until (InputStream &source, std::function< bool(char)> criterion)
	Lexing function that advances the stream until its current char fulfills the provided criterion. More...
template<typename InputStream >
void	skip_while (InputStream &source, char criterion)
	Lexing function that advances the stream while its current char equals the provided one. More...
template<typename InputStream >
void	skip_while (InputStream &source, std::function< bool(char)> criterion)
	Lexing function that advances the stream while its current char fulfills the provided criterion. More...
template<typename RandomAccessIterator >
std::vector< size_t >	sort_indices (RandomAccessIterator first, RandomAccessIterator last)
	Get the indices to the sorted order of the given range. More...
template<typename RandomAccessIterator , typename Comparator >
std::vector< size_t >	sort_indices (RandomAccessIterator first, RandomAccessIterator last, Comparator comparator)
	Get the indices to the sorted order of the given range. More...
template<typename RandomAccessIterator >
void	sort_natural (RandomAccessIterator first, RandomAccessIterator last, bool reverse=false)
	Sort a range of std::string (or convertible to std::string) elements, using natural sorting; see compare_natural(). More...
template<class RandomAccessIteratorA , class RandomAccessIteratorB >
double	spearmans_rank_correlation_coefficient (RandomAccessIteratorA first_a, RandomAccessIteratorA last_a, RandomAccessIteratorB first_b, RandomAccessIteratorB last_b)
	Calculate Spearman's Rank Correlation Coefficient between two ranges of double. More...
double	spearmans_rank_correlation_coefficient (std::vector< double > const &vec_a, std::vector< double > const &vec_b)
	Calculate Spearman's Rank Correlation Coefficient between the entries of two vectors. More...
std::vector< std::string >	split (std::string const &str, char delimiter='\t', const bool trim_empty=true)
	Spilt a string into parts, given a delimiter char. More...
std::vector< std::string >	split (std::string const &str, std::function< bool(char)> delimiter_predicate, const bool trim_empty=true)
	Spilt a string into parts, given a delimiter_predicate that returns true for delimiters chars. More...
std::vector< std::string >	split (std::string const &str, std::string const &delimiters, const bool trim_empty=true)
	Spilt a string into parts, given a delimiters set of chars. More...
static std::vector< std::string >	split_ (std::string const &string, std::function< size_t(std::string const &, size_t)> find_pos, size_t advance_by, const bool trim_empty)
	Local function that does the work for the split cuntions. More...
std::vector< std::string >	split_at (std::string const &str, std::string const &delimiter, const bool trim_empty=true)
	Spilt a string into parts, given a delimiter string. More...
std::vector< size_t >	split_range_list (std::string const &str)
	Split a string containing positive interger numbers into its parts and resolve ranges. More...
constexpr double	squared (double x)
	Square of a number. More...
template<typename RandomAccessIterator >
std::vector< size_t >	stable_sort_indices (RandomAccessIterator first, RandomAccessIterator last)
	Get the indices to the stable sorted order of the given range. More...
template<typename RandomAccessIterator , typename Comparator >
std::vector< size_t >	stable_sort_indices (RandomAccessIterator first, RandomAccessIterator last, Comparator comparator)
	Get the indices to the stable sorted order of the given range. More...
std::vector< MeanStddevPair >	standardize_cols (Matrix< double > &data, bool scale_means=true, bool scale_std=true)
	Standardize the columns of a Matrix by subtracting the mean and scaling to unit variance. More...
std::vector< MeanStddevPair >	standardize_rows (Matrix< double > &data, bool scale_means=true, bool scale_std=true)
	Standardize the rows of a Matrix by subtracting the mean and scaling to unit variance. More...
bool	starts_with (std::string const &text, std::string const &prefix)
	Return whether a string starts with another string, i.e., check for a prefix. More...
bool	starts_with (std::string const &text, std::string const &prefix, std::string &suffix)
	Return whether a string starts with another string, i.e., check for a prefix. More...
bool	starts_with_ci (std::string const &text, std::string const &prefix)
	Return whether a string starts with another string, i.e., check for a prefix, case insensitive. More...
bool	starts_with_ci (std::string const &text, std::string const &prefix, std::string &suffix)
	Return whether a string starts with another string, i.e., check for a prefix, case insensitive. More...
bool	starts_with_ci_alnum (std::string const &text, std::string const &prefix)
	Return whether a string starts with another string (prefix), comparing case-independent, and ignoring all non-alphanumerical characters. More...
bool	starts_with_ci_alnum (std::string const &text, std::string const &prefix, std::string &suffix, bool trim_suffix=false)
	Return whether a string starts with another string (prefix), comparing case-independent, and ignoring all non-alphanumerical characters. More...
int	strcasecmp (char const *s1, char const *s2)
	Compares two strings, ignoring case differences. More...
static std::string	strerror_ ()
	Overload of error-reporting function, to enable use with VS. More...
int	strncasecmp (char const *s1, char const *s2, size_t n)
	Compares up to n chars of two strings, ignoring case differences. More...
double	sum (const Histogram &h)
std::string	summarize_column (Dataframe const &df, size_t col_index)
std::string	summarize_column (Dataframe const &df, std::string const &col_name)
std::string	summarize_column_common_ (Dataframe const &df, size_t col_index, std::string const &description)
template<typename T >
std::string	summarize_column_double_ (Dataframe const &df, size_t col_index)
template<typename T >
std::string	summarize_column_int_ (Dataframe const &df, size_t col_index)
std::string	summarize_column_string_ (Dataframe const &df, size_t col_index)
std::string	summarize_columns (Dataframe const &df)
Matrix< double >	sums_of_squares_and_cross_products_matrix (Matrix< double > const &data)
	Calculate the Sums of Squares and Cross Products Matrix (SSCP Matrix). More...
std::string	svg_arc (double center_x, double center_y, double radius, double start_angle, double end_angle, bool wedge=false)
	Create an arc to use in an SvgPath. More...
template<typename T >
std::string	svg_attribute (std::string const &name, T const &value, std::string const &unit="")
SvgBox	svg_bounding_box (std::vector< SvgPoint > const &points)
	Compute the bounding box of a set of points. More...
SvgBox	svg_bounding_box (std::vector< SvgPoint > const &points, SvgTransform const &transform)
	Compute the bounding box of a set of points, including their transformation. More...
std::string	svg_comment (std::string const &content)
std::string	svg_data_uri (std::string const &media_type, std::string const &content, bool encode_base64=false)
template<typename T , typename Traits >
void	swap (BlockingConcurrentQueue< T, Traits > &a, BlockingConcurrentQueue< T, Traits > &b) MOODYCAMEL_NOEXCEPT
void	swap (Color &lhs, Color &rhs)
template<typename T , typename Traits >
void	swap (ConcurrentQueue< T, Traits > &a, ConcurrentQueue< T, Traits > &b) noexcept
void	swap (ConsumerToken &a, ConsumerToken &b) noexcept
void	swap (Histogram &lhs, Histogram &rhs)
void	swap (HistogramAccumulator &lhs, HistogramAccumulator &rhs)
void	swap (NexusTaxa &lhs, NexusTaxa &rhs)
void	swap (NexusTrees &lhs, NexusTrees &rhs)
template<typename T >
void	swap (Optional< T > &x, Optional< T > &y)
void	swap (ProducerToken &a, ProducerToken &b) noexcept
void	swap (Style &lhs, Style &rhs)
template<typename T , typename Traits >
void	swap (typename ConcurrentQueue< T, Traits >::ImplicitProducerKVP &a, typename ConcurrentQueue< T, Traits >::ImplicitProducerKVP &b) noexcept
template<typename T >
void	swap_cols (Matrix< T > &data, size_t col_a, size_t col_b)
	Swap (interchange) two columns of a Matrix, given their indices. More...
template<typename T >
void	swap_rows (Matrix< T > &data, size_t row_a, size_t row_b)
	Swap (interchange) two rows of a Matrix, given their indices. More...
static bool	symlink_resolve_ (const std::string &start, std::string &end)
Bitvector	symmetric_difference (Bitvector const &lhs, Bitvector const &rhs)
std::string	tail (std::string const &text, size_t lines=10)
	Return the last lines of the text. More...
template<typename ForwardIterator >
std::vector< std::tm >	time_to_tm (ForwardIterator first, ForwardIterator last, bool use_local_time=false, size_t size=0)
	Convert a list of std::time_t objects to a std::vector of std::tm objects. More...
std::tm	time_to_tm (std::time_t const &time, bool use_local_time=false)
	Convert std::time_t object to a std::tm object. More...
std::vector< std::tm >	time_to_tm (std::vector< std::time_t > const &times, bool use_local_time=false)
	Convert a std::vector of std::time_t objects to a std::vector of std::tm objects. More...
std::string	tm_date_to_string (std::tm const &time)
	Print the given std::tm object as a std::string containing only the date, using the ISO 8601 extended format. More...
std::string	tm_time_to_string (std::tm const &time)
	Print the given std::tm object as a std::string containing only the time, using the ISO 8601 extended format. More...
std::string	tm_to_string (std::tm const &time)
	Print the given std::tm object as a std::string, using the ISO 8601 extended format. More...
std::string	tm_to_string (std::tm const &time, std::string const &format)
	Print the given std::tm object as a std::string, using the format. More...
std::string	tm_to_string (std::tm const &time, std::string const &format, std::string const &locale)
	Print the given std::tm object as a std::string, using the format and locale. More...
template<typename ForwardIterator >
std::vector< std::time_t >	tm_to_time (ForwardIterator first, ForwardIterator last, bool use_local_time=false, size_t size=0)
	Convert a list of std::tm objects to a std::vector of std::time_t objects. More...
std::time_t	tm_to_time (std::tm time, bool use_local_time=false)
	Convert std::tm object to a std::time_t object. More...
std::vector< std::time_t >	tm_to_time (std::vector< std::tm > const &times, bool use_local_time=false)
	Convert a std::vector of std::tm objects to a std::vector of std::time_t objects. More...
template<typename T >
std::string	to_bit_string (T const x, char const zero='0', char const one='1', bool const byte_space=true)
	Return the bit representation of an unsigned int. More...
std::shared_ptr< BaseOutputTarget >	to_file (std::string const &file_name, GzipCompressionLevel compression_level, bool auto_adjust_filename=true)
	Obtain an output target for writing to a file. More...
std::shared_ptr< BaseOutputTarget >	to_file (std::string const &file_name, std::ios_base::openmode mode=std::ios_base::out)
	Obtain an output target for writing to a file, using a specific output mode. More...
std::shared_ptr< BaseOutputTarget >	to_gzip_block_file (std::string const &file_name, std::size_t block_size=GzipBlockOStream::GZIP_DEFAULT_BLOCK_SIZE, GzipCompressionLevel compression_level=GzipCompressionLevel::kDefaultCompression, std::shared_ptr< ThreadPool > thread_pool=nullptr, bool auto_adjust_filename=true)
	Obtain an output target for writing gzip block compressed data to a file. More...
std::shared_ptr< BaseOutputTarget >	to_gzip_file (std::string const &file_name)
	Obtain an output target for writing to a gzip-compressed file. More...
constexpr char	to_lower (char c) noexcept
	Return the lower case version of a letter, ASCII-only. More...
std::string	to_lower (std::string const &str)
	Return an all-lowercase copy of the given string, locale-aware. More...
std::string	to_lower_ascii (std::string const &str)
	Return an all-lowercase copy of the given string, ASCII-only. More...
void	to_lower_ascii_inplace (std::string &str)
	Turn the given string to all-lowercase, ASCII-only. More...
void	to_lower_inplace (std::string &str)
	Turn the given string to all-lowercase, locale-aware. More...
std::string	to_nucleic_acids (TwobitVector const &vec)
	Turn a TwobitVector into its string representation of nucleic acids. More...
std::shared_ptr< BaseOutputTarget >	to_stderr ()
	Obtain an output target for writing to standard error (i.e., stderr or cerr). More...
std::shared_ptr< BaseOutputTarget >	to_stdout ()
	Obtain an output target for writing to standard output (i.e., stdout or cout). More...
std::shared_ptr< BaseOutputTarget >	to_stream (std::ostream &target_stream, GzipCompressionLevel compression_level=GzipCompressionLevel::kNoCompression)
	Obtain an output target for writing to a stream. More...
std::shared_ptr< BaseOutputTarget >	to_string (std::string &target_string)
	Obtain an output target for writing to a string. More...
std::string	to_string_byte_format (size_t value)
	Produce a human readable formatting of a size in bytes, using the appropriate suffix. More...
std::string	to_string_leading_zeros (size_t value, size_t length=6)
	Return a string representation of a size_t value with a fixed length, that is, by adding leading zeros. More...
template<typename T >
std::string	to_string_nice (T const &v)
	Return a string representation of a given value. More...
std::string	to_string_precise (double value, int precision=6)
	Return a precise string representation of the input value, using the provided precision value (determining its decimal places). More...
std::string	to_string_rounded (double value, int precision=6)
	Return a string representation of the input value, using the provided precision value (determining its decimal places) to round, and truncate trailing zeros. More...
constexpr char	to_upper (char c) noexcept
	Return the upper case version of a letter, ASCII-only. More...
std::string	to_upper (std::string const &str)
	Return an all-uppercase copy of the given string, locale-aware. More...
std::string	to_upper_ascii (std::string const &str)
	Return an all-uppercase copy of the given string, ASCII-only. More...
void	to_upper_ascii_inplace (std::string &str)
	Turn the given string to all-uppercase, ASCII-only, inline. More...
void	to_upper_inplace (std::string &str)
	Turn the given string to all-uppercase, locale-aware. More...
TwobitVector::ValueType	translate_from_nucleic_acid (char site)
	Translate a char into TwobitVector::ValueType. More...
char	translate_to_nucleic_acid (TwobitVector::ValueType value)
	Translate a TwobitVector::ValueType into its char representation. More...
template<typename T >
Matrix< T >	transpose (Matrix< T > const &mat)
	Transpose a Matrix. More...
template<typename T >
void	transpose_inplace (Matrix< T > &mat)
	Transpose a Matrix inplace, without allocating a new Matrix. More...
size_t	triangular_index (size_t i, size_t j, size_t n)
	Given indices i and j in a quadratic Matrix, find the corresponding linear index. More...
std::pair< size_t, size_t >	triangular_indices (size_t k, size_t n)
	Given a linear index in a upper triangular Matrix, find the corresponding Matrix indices. More...
size_t	triangular_size (size_t n)
	Calculate the number of linear indices needed for a triangular Matrix of size n. More...
void	tridiagonal_ql_algorithm (Matrix< double > &data, TridiagonalDecompositionData &tri, size_t max_iterations=1000)
	Reduce a symmetric matrix to a symmetric tridiagonal matrix. More...
std::string	trim (std::string const &s, std::string const &delimiters=" \f\n\r\t\v")
	Return a copy of the input string, with trimmed white spaces (or any other delimiters). More...
std::string	trim_left (std::string const &s, std::string const &delimiters=" \f\n\r\t\v")
	Return a copy of the input string, with right trimmed white spaces (or any other delimiters). More...
std::string	trim_right (std::string const &s, std::string const &delimiters=" \f\n\r\t\v")
	Return a copy of the input string, with left trimmed white spaces (or any other delimiters). More...
std::vector< double >	udu_transpose_ (size_t M, std::vector< double > const &U, double scale)
	Calculate U.D.U-transpose. More...
std::vector< double >	udvdu_transpose_ (size_t M, std::vector< double > const &U, std::vector< double > const &V, double scale)
	Calculate U.D.V.D.U-transpose. More...
bool	validate (Dataframe const &df)
template<class ForwardIterator >
double	weighted_arithmetic_mean (ForwardIterator first_value, ForwardIterator last_value, ForwardIterator first_weight, ForwardIterator last_weight)
	Calculate the weighted arithmetic mean of a range of double values. More...
double	weighted_arithmetic_mean (std::vector< double > const &values, std::vector< double > const &weights)
	Calculate the weighted arithmetic mean of a std::vector of double elements. More...
template<class ForwardIterator >
double	weighted_geometric_mean (ForwardIterator first_value, ForwardIterator last_value, ForwardIterator first_weight, ForwardIterator last_weight)
	Calculate the weighted geometric mean of a range of positive numbers. More...
double	weighted_geometric_mean (std::vector< double > const &values, std::vector< double > const &weights)
	Calculate the weighted geometric mean of a std::vector of double elements. More...
template<class ForwardIterator >
double	weighted_harmonic_mean (ForwardIterator first_value, ForwardIterator last_value, ForwardIterator first_weight, ForwardIterator last_weight, HarmonicMeanZeroPolicy zero_policy=HarmonicMeanZeroPolicy::kThrow)
	Calculate the weighted harmonic mean of a range of positive numbers. More...
double	weighted_harmonic_mean (std::vector< double > const &values, std::vector< double > const &weights, HarmonicMeanZeroPolicy zero_policy=HarmonicMeanZeroPolicy::kThrow)
	Calculate the weighted harmonic mean of a std::vector of double elements. More...
double	weighted_inner_product (std::vector< double > const &x_input, std::vector< double > const &y_input, std::vector< double > const &weights=std::vector< double >{})
	(Weighted) inner product of two vectors. More...
GlmFreedom	weighted_mean_centering (std::vector< double > const &y_input, std::vector< double > const &weights, std::vector< size_t > const &strata, bool with_intercept, bool centering, std::vector< double > &y_output)
	(Weighted) mean and centering. More...
double	weighted_residuals (std::vector< double > const &x_input, std::vector< double > const &y_input, std::vector< double > const &weights, std::vector< double > &y_output)
	Calculate the residuals from (weighted) regression through the origin. More...
double	weighted_sum (std::vector< double > const &x_input, std::vector< double > const &weights=std::vector< double >{})
	(Weighted) sum of a vector of values. More...
double	weighted_sum_of_squares (std::vector< double > const &x_input, std::vector< double > const &weights=std::vector< double >{})
	(Weighted) sum of squares. More...
std::string	wrap (std::string const &text, size_t line_length=80)
	Wrap a text at a given line_length. More...
uint64_t	xgetbv (unsigned int index)
template<typename T >
std::string	xml_attribute (std::string const &name, T const &value)
std::string	xml_comment (std::string const &content)
std::string	xml_deescape (std::string const &txt)
	De-escape special XML characters. More...
std::string	xml_escape (std::string const &txt)
	Escape special XML characters. More...
const XmlComment *	xml_value_to_comment (const XmlValue *v)
	Converts a pointer to an XmlValue to XmlComment if appropriate. More...
const XmlElement *	xml_value_to_element (const XmlValue *v)
	Converts a pointer to an XmlValue to XmlElement if appropriate. More...
const XmlMarkup *	xml_value_to_markup (const XmlValue *v)
	Converts a pointer to an XmlValue to XmlMarkup if appropriate. More...

Enumerations
enum	ColorListDiverging {   kBrbg, kPiyg, kPrgn, kPuor,   kRdbu, kRdgy, kRdylbu, kRdylgn,   kSpectral }
enum	ColorListMisc { kNextstrain }
enum	ColorListQualitative {   kAccent, kDark2, kPaired, kPastel1,   kPastel2, kSet1, kSet2, kSet3 }
enum	ColorListSequential {   kBupubk, kBlues, kBugn, kBupu,   kGnbu, kGreens, kGreys, kOranges,   kOrrd, kPubu, kPubugn, kPurd,   kPurples, kRdpu, kReds, kYlgn,   kYlgnbu, kYlorbr, kYlorrd, kHeat,   kMagma, kInferno, kPlasma, kViridis }
enum	GeoCoordinateComponent { kLatitude, kLongitude }
	Local helper enum that indicates which component of a coordinate we are dealing with. More...
enum	GzipCompressionLevel : int { kDefaultCompression = -1, kNoCompression = 0, kBestSpeed = 1, kBestCompression = 9 }
	List of possible compression levels used for GzipOStream. More...
enum	HarmonicMeanZeroPolicy { kThrow, kIgnore, kReturnZero, kCorrection }
	Select a policy on how to treat zeroes in the computation of harmonic_mean() and weighted_harmonic_mean(). More...
enum	HashingFunctions { kMD5, kSHA1, kSHA256 }
	List of the currently implemented hashing functions. More...
enum	KendallsTauMethod { kTauA, kTauB, kTauC }
	Method for computing Kendall's Tau. More...
enum	KmeansInitializationStrategy { kRandomAssignments, kRandomCentroids, kKmeansPlusPlus, kNone }
	Enum of the initialization strategies offered by the Kmeans implementation. More...
enum	MdsAlgorithm { kUcf, kSmacof }
	Choice of algorithm to use for Multi-Dimensional Scaling (MDS). More...
enum	PcaStandardization { kCorrelation, kCovariance, kSSCP }
	Setting for principal_component_analysis() to determine which form of standardization of the data to use prior to perfoming the PCA. More...
enum	RedBackColor { kInvalid, kRed, kBlack, kKDoubleBlack }
	Definition for Red-Black Tree coloring. More...
enum	SkipWhitespace : unsigned char { kNone = 0, kLeading = 1, kTrailing = 2, kSurrounding = 3 }
	Option to determine how to treat surrounding whitespace when scanning an input stream. More...

Typedefs
using	DefaultIntervalNumericalType = int
	Default numerical type to use in an Interval. More...
using	InputReader = AsynchronousReader
	Alias for the either AsynchronousReader or SynchronousReader. More...
using	KahanSum = CompensatedSum< KahanSummation >
	Typedef shorthand for a Kahan sum. More...
using	KleinSum = CompensatedSum< KleinSummation >
	Typedef shorthand for a Kahan Babushka Klein sum. More...
using	NamedColorList = std::vector< std::pair< std::string, ColorBytes > >
using	NeumaierSum = CompensatedSum< NeumaierSummation >
	Typedef shorthand for a Kahan Babushka Neumaier sum. More...

Variables
static const std::array< std::string, 128 >	ascii_names_
	List of all ASCII names. More...
static const std::array< std::string, 128 >	ascii_symbols_
	List of all ASCII symbols. More...
static const char	base64_encode_lookup_ []
static const char	base64_pad_char_ = '='
const std::vector< Color >	color_list_accent_
const std::vector< Color >	color_list_blues_
const std::vector< Color >	color_list_brbg_
const std::vector< Color >	color_list_bugn_
const std::vector< Color >	color_list_bupu_
const std::vector< Color >	color_list_bupubk_
	Our own color list used for visualizing trees. More...
const std::vector< Color >	color_list_dark2_
const std::vector< Color >	color_list_gnbu_
const std::vector< Color >	color_list_greens_
const std::vector< Color >	color_list_greys_
const std::vector< Color >	color_list_heat_
const std::vector< Color >	color_list_inferno_
const NamedColorList	color_list_lego_
	Struct that stores a static const map of named LEGO colors. More...
const std::vector< Color >	color_list_magma_
static const std::vector< Color >	color_list_nextstrain_256_
const std::vector< Color >	color_list_oranges_
const std::vector< Color >	color_list_orrd_
const std::vector< Color >	color_list_paired_
const std::vector< Color >	color_list_pastel1_
const std::vector< Color >	color_list_pastel2_
const std::vector< Color >	color_list_piyg_
const std::vector< Color >	color_list_plasma_
const std::vector< Color >	color_list_prgn_
const std::vector< Color >	color_list_pubu_
const std::vector< Color >	color_list_pubugn_
const std::vector< Color >	color_list_puor_
const std::vector< Color >	color_list_purd_
const std::vector< Color >	color_list_purples_
const std::vector< Color >	color_list_rdbu_
const std::vector< Color >	color_list_rdgy_
const std::vector< Color >	color_list_rdpu_
const std::vector< Color >	color_list_rdylbu_
const std::vector< Color >	color_list_rdylgn_
const std::vector< Color >	color_list_reds_
const std::vector< Color >	color_list_set1_
const std::vector< Color >	color_list_set2_
const std::vector< Color >	color_list_set3_
const std::vector< Color >	color_list_spectral_
const std::vector< Color >	color_list_viridis_
const NamedColorList	color_list_web_
	Struct that stores a static const map of named web colors. More...
const NamedColorList	color_list_xkcd_
	Struct that stores a static const map of named xkcd colors. More...
const std::vector< Color >	color_list_ylgn_
const std::vector< Color >	color_list_ylgnbu_
const std::vector< Color >	color_list_ylorbr_
const std::vector< Color >	color_list_ylorrd_
static const std::vector< std::vector< Color > >	color_lists_nextstrain_1_16_
constexpr double	EARTH_MEAN_RADIUS = 6371.0
	Earth is not flat! More...
static const std::array< std::string, 9 >	formats_
static std::mutex	genesis_log_mutex_
static const std::size_t	GZIP_DEFAULT_BUFFER_SIZE = (std::size_t) 1 << 20
	Default buffer size for all gzip (de)compression buffers. More...
static const std::array< std::string, 3 >	locales_ = {{ "C", "en_US.UTF-8", "" }}
static const std::array< double, 1024 >	log_factorial_lookup_
	Log-factorial log(x!) lookup table for fast computation of binomial coefficients. See binomial_coefficient_approx() for usage, and see log_factorial_lookup_generator_() for the generator function. More...
constexpr double	MDS_EPSILON = 0.0000001
const nullopt_t	nullopt ((nullopt_t::init()))
	Optional to indicate an empty value. More...
static const uint64_t	pcg32_increment = 1442695040888963407u
static const uint64_t	pcg32_multiplier = 6364136223846793005u
static uint64_t	pcg32_state = 0x4d595df4d0f33173
constexpr double	PI = 3.141592653589793238463
	Make the world go round. More...
static std::mutex	tm_mutex_
	The std::localtime and std::gmtime functions are not thread safe, due to their shared internal state. Make sure that we can use them from multiple threads. More...

Function Documentation

abs_diff()

constexpr T genesis::utils::abs_diff ( T const &  lhs, T const &  rhs  )

inlineconstexpr

Calculate the absolute differenence between two values.

This function is particularly useful for unsigned types, as subtracting them and then using std::abs() does not work for them.

Definition at line 95 of file common.hpp.

affirm_char_or_throw() [1/2]

void genesis::utils::affirm_char_or_throw ( InputStream &  source, char  criterion, SkipWhitespace  skip_ws = SkipWhitespace::kNone  )

inline

Lexing function that checks whether the current char from the stream equals the provided one.

If not, the function throws std::runtime_error. The stream is not advanced (i.e., it stays at its current position). For a similar function that reads (i.e., also advances) the current char from the stream, see read_char_or_throw().

Using the parameter skip_ws, it is possible to skip leading and/or trailing whitespaces before/after treating the criterion char. See SkipWhitespace for more information.

Definition at line 385 of file scanner.hpp.

affirm_char_or_throw() [2/2]

void genesis::utils::affirm_char_or_throw ( InputStream &  source, std::function< bool(char)>  criterion, SkipWhitespace  skip_ws = SkipWhitespace::kNone  )

inline

Lexing function that checks whether the current char from the stream fulfills the provided criterion.

If not, the function throws std::runtime_error. The stream is not advanced (i.e., it stays at its current position). For a similar function that reads (i.e., also advances) the current char from the stream, see read_char_or_throw().

Using the parameter skip_ws, it is possible to skip leading and/or trailing whitespaces before/after treating the criterion char. See SkipWhitespace for more information.

Definition at line 422 of file scanner.hpp.

aitchison_norm() [1/2]

double genesis::utils::aitchison_norm	(	ForwardIterator	first,
		ForwardIterator	last
	)

Calculate the Aitchison norm of a range of positive numbers.

The iterators first and last need to point to a range of double values, with last being the past-the-end element.

Following [1], the Aitchison norm \( \| x \|_a \) of a vector \( x \) with \( s \) elements is caluclated as

\( \| x \|_a = \sqrt{ \frac{1}{2s} \sum_{j=1}^{s} \sum_{k=1}^{s} \left( \ln{ \frac{x_j}{x_k} } \right)^2 } \)

That is, the calculation is in \( \mathcal{O}( s^2 ) \).

[1] V. Pawlowsky-Glahn, J. J. Egozcue, and R. Tolosana-Delgado, "Modelling and Analysis of Compositional Data". Chichester, UK: John Wiley & Sons, Ltd, 2015. https://onlinelibrary.wiley.com/doi/book/10.1002/9781119003144

See also

p_norm(), euclidean_norm(), manhattan_norm(), and maximum_norm() for some standard norms.

Definition at line 216 of file distance.hpp.

aitchison_norm() [2/2]

double genesis::utils::aitchison_norm ( std::vector< double > const &  vec )

inline

Calculate the Aitchison norm of a std::vector of double elements.

See also

aitchison_norm( ForwardIterator, ForwardIterator ) for details.

Definition at line 262 of file distance.hpp.

almost_equal_relative()

bool genesis::utils::almost_equal_relative ( double  lhs, double  rhs, double  max_rel_diff = std::numeric_limits<double>::epsilon()  )

inline

Check whether two doubles are almost equal, using a relative epsilon to compare them.

Definition at line 157 of file common.hpp.

arithmetic_mean() [1/2]

double genesis::utils::arithmetic_mean	(	ForwardIterator	first,
		ForwardIterator	last
	)

Calculate the arithmetic mean of a range of numbers.

The iterators first and last need to point to a range of double values, with last being the past-the-end element. The function then calculates the arithmetic mean of all finite elements in the range. If no elements are finite, or if the range is empty, the returned value is 0.0. Non-finite numbers are ignored.

See also

arithmetic_mean( std::vector<double> const& ) for a version for std::vector.

mean_stddev() for a function that also calculates the standard deviation.

geometric_mean() for a function that calculates the geometric mean, and

harmonic_mean() for a function that calculates the harmonic mean.

weighted_arithmetic_mean() for a function that calculates the weighted arithmetic mean.

Definition at line 438 of file statistics.hpp.

arithmetic_mean() [2/2]

double genesis::utils::arithmetic_mean ( std::vector< double > const &  vec )

inline

Calculate the arithmetic mean of a std::vector of double elements.

See also

arithmetic_mean( ForwardIterator first, ForwardIterator last ) for details.

mean_stddev() for a function that simultaneously calculates the standard deviation.

geometric_mean() for a function that calculates the geometric mean, and

harmonic_mean() for a function that calculates the harmonic mean.

Definition at line 473 of file statistics.hpp.

ascending()

void genesis::utils::ascending ( T &  f, T &  s  )

inline

Sort two values in ascending order, inplace.

Definition at line 70 of file common.hpp.

base64_decode_()

T genesis::utils::base64_decode_

(

std::string const &

input

)

Definition at line 152 of file base64.cpp.

base64_decode_string()

std::string base64_decode_string

(

std::string const &

input

)

Definition at line 283 of file base64.cpp.

base64_decode_uint8()

std::vector< std::uint8_t > base64_decode_uint8

(

std::string const &

input

)

Definition at line 277 of file base64.cpp.

base64_encode() [1/2]

std::string base64_encode	(	std::string const &	input,
		size_t	line_length
	)

Definition at line 272 of file base64.cpp.

base64_encode() [2/2]

std::string base64_encode	(	std::vector< std::uint8_t > const &	input,
		size_t	line_length
	)

Definition at line 267 of file base64.cpp.

base64_encode_()

std::string genesis::utils::base64_encode_	(	T const &	input,
		size_t	line_length
	)

Definition at line 52 of file base64.cpp.

binary_find()

ForwardIt genesis::utils::binary_find	(	ForwardIt	first,
		ForwardIt	last,
		const T &	value,
		Compare	comp = {}
	)

Binary search on a sorted/partitioned range, returns an iterator to the element if found.

See https://en.cppreference.com/w/cpp/algorithm/lower_bound for details.

Definition at line 56 of file algorithm.hpp.

binomial_coefficient()

double genesis::utils::binomial_coefficient ( size_t  n, size_t  k  )

inline

Compute the binomial coefficient, that is n choose k, for two integer numbers, for large numbers.

The precise integer function binomial_coefficient_int() can only handle values up to n == 62 (for non-small k at least). That is, at n == 63, k == 29, we have exhausted the range of 64bit numbers.

To also be able to work with larger n and k, we here offer an approximation that returns a double value instead, and hence can compute binomial coefficients of up to n == 1029 (exclusive) for all values of k, which for k == n/2 is about as large as double precision allows. The approximation is not quite up to double precision, and returns values with an error roughly in the range of e-12 for large numbers.

For n > 1029, we attempt to compute this, which will work for smaller values of k. In case this overflows the double precision range, positive infinity is returned instead. The first such combination is n==1030 and k==500, causing inf to be returned.

The returned values for all n and k that are also valid with the integer version binomial_coefficient_int() yield identical results (up to float precision). That is, in particular for all n < 63, as well as for larger n with small k. Note furthermore that we use a lookup table of factorials for the bulk of the computation here. Hence, for larger numbers, this function is also faster than explicity computing the values.

See also log_binomial_coefficient() for the log-space variant of this function.

Definition at line 99 of file binomial.hpp.

binomial_coefficient_check_n_k_()

void genesis::utils::binomial_coefficient_check_n_k_ ( size_t  n, size_t  k  )

inline

Local helper function to check that n and k are valid for a binomial coefficient.

Definition at line 427 of file binomial.cpp.

binomial_coefficient_int()

size_t binomial_coefficient_int	(	size_t	n,
		size_t	k
	)

Compute the binomial coefficient, that is n choose k, for two integer numbers.

The function throws for invalid arguments (n or k equal to 0, or k larger than n), or on overflow. For all n < 63, this does not overflow with 64 bit numbers.

Definition at line 458 of file binomial.cpp.

binomial_distribution()

double genesis::utils::binomial_distribution ( size_t  k, size_t  n, double  p  )

inline

Compute the probability mass function for a binomial distribution.

Note that we reverse the order of k and n here compared to binomial_coefficient() here, in order to comply with common notation.

We are working in log-space for the main part of the computation, and only translate back at the very end. For large n, we are attempting to compute the distribution, but it might underflow. See binomial_coefficient() for details.

Definition at line 121 of file binomial.hpp.

bitstring() [1/2]

std::string bitstring

(

TwobitVector const &

vec

)

Return a string with a bit-representation of a TwobitVector.

It returns the words of the vector with bits in the order of the underlying integer type. This is mainly useful for debugging and testing.

Definition at line 124 of file utils/math/twobit_vector/functions.cpp.

bitstring() [2/2]

std::string bitstring

(

TwobitVector::WordType const &

vec

)

Return a string with a bit-representation of a TwobitVector::WordType.

It returns the word with bits in the order of the underlying integer type. This is mainly useful for debugging and testing.

Definition at line 140 of file utils/math/twobit_vector/functions.cpp.

bitwise_and()

Bitvector bitwise_and	(	Bitvector const &	lhs,
		Bitvector const &	rhs,
		bool	use_larger = false
	)

Take the bitwise and of two Bitvectors of potentially different size.

The function is the same as the normal version, but allows to use Bitvectors of different sizes. By default (use_larger == false), we use the number of bits of the shorter Bitvector, that is, it operates on bits [ 0 , m ) with m = min( lhs.size(), rhs.size() ). If use_larger is set however, the resulting Bitvector has the max size of the two inputs, with the bits at the end (the ones after m) being false.

Definition at line 45 of file utils/math/bitvector/operators.cpp.

bitwise_or()

Bitvector bitwise_or	(	Bitvector const &	lhs,
		Bitvector const &	rhs,
		bool	use_larger = false
	)

Take the bitwise or of two Bitvectors of potentially different size.

The function is the same as the normal version, but allows to use Bitvectors of different sizes. By default (use_larger == false), we use the number of bits of the shorter Bitvector, that is, it operates on bits [ 0 , m ) with m = min( lhs.size(), rhs.size() ). If use_larger is set however, the resulting Bitvector has the max size of the two inputs, with the bits at the end (the ones after m) being false.

Definition at line 58 of file utils/math/bitvector/operators.cpp.

bitwise_xor()

Bitvector bitwise_xor	(	Bitvector const &	lhs,
		Bitvector const &	rhs,
		bool	use_larger = false
	)

Take the bitwise xor of two Bitvectors of potentially different size.

The function is the same as the normal version, but allows to use Bitvectors of different sizes. By default (use_larger == false), we use the number of bits of the shorter Bitvector, that is, it operates on bits [ 0 , m ) with m = min( lhs.size(), rhs.size() ). If use_larger is set however, the resulting Bitvector has the max size of the two inputs, with the bits at the end (the ones after m) being false.

Definition at line 71 of file utils/math/bitvector/operators.cpp.

build_path_base_swap_()

static void genesis::utils::build_path_base_swap_ ( std::string &  path, const std::string &  newbase  )

static

Definition at line 608 of file fs.cpp.

char_match_ci()

constexpr bool genesis::utils::char_match_ci ( char  c1, char  c2  )

constexprnoexcept

Return whether two chars are the same, case insensitive, and ASCII-only.

Definition at line 243 of file char.hpp.

char_to_hex() [1/2]

std::string char_to_hex	(	char	c,
		bool	full = true
	)

Return the name and hex representation of a char.

This is meant for user output, for example to warn about invalid input characters. Hence, by default, a text-representation is returned, using the form

LF (0x0A; control: NL line feed, new line)
'N' (0x4E; letter: capital N)

where non-printable characters are abbreviated by their symbol, and printable characters are included in single quotation marks.

Non-ASCII characters (those outside of the 0-127 interval) are written in the form

non-ASCII char (0xF7)

If full is set to false, just the two-byte hex presentation is returned (e.g., 4E for N).

Definition at line 118 of file char.cpp.

char_to_hex() [2/2]

std::string char_to_hex	(	unsigned char	c,
		bool	full = true
	)

Return the name and hex representation of a char, given as an unsigned char.

This overload is meant for situations were a text input is read from file as unsigned char. The rest of the function is identical to char_to_hex( char, bool ), see there for details.

Definition at line 136 of file char.cpp.

chdir_getcwd_()

static std::string genesis::utils::chdir_getcwd_ ( std::string const &  dir )

static

Definition at line 541 of file fs.cpp.

check_mode_()

static void genesis::utils::check_mode_ ( std::string const &  filename, std::ios_base::openmode  mode  )

static

Definition at line 157 of file strict_fstream.cpp.

check_open_()

static void genesis::utils::check_open_ ( std::ios *  s_p, std::string const &  filename, std::ios_base::openmode  mode  )

static

Definition at line 177 of file strict_fstream.cpp.

check_peek_()

static void genesis::utils::check_peek_ ( std::istream *  is_p, std::string const &  filename, std::ios_base::openmode  mode  )

static

Definition at line 188 of file strict_fstream.cpp.

circumference()

double genesis::utils::circumference ( double  radius )

inline

Definition at line 57 of file common.hpp.

closure() [1/2]

void genesis::utils::closure	(	ForwardIterator	first,
		ForwardIterator	last
	)

Calculate the closure of a range of numbers.

The iterators first and last need to point to a range of double values, with last being the past-the-end element. Then, the closure [1] of the elements is calculated, that is, they are all divided by their total sum. This is used in compositional data analysis. Non-finite elements are ignored, negative elements throw an exception.

[1] J. Aitchison, "The statistical analysis of compositional data". Chapman and Hall London, 1986. https://www.jstor.org/stable/2345821

Definition at line 288 of file statistics.hpp.

closure() [2/2]

void genesis::utils::closure ( std::vector< double > &  vec )

inline

Calculate the closure of a std::vector of double elements.

See also

closure( ForwardIterator first, ForwardIterator last ) for details.

Definition at line 330 of file statistics.hpp.

coefficient_of_variation() [1/2]

double genesis::utils::coefficient_of_variation ( MeanStddevPair const &  ms )

inline

Calculate the index of dispersion.

The coefficient of variation (CV), also known as the relative standard deviation (RSD), is defined as the ratio of the standard deviation to the mean. See mean_stddev() to calculate those values. See https://en.wikipedia.org/wiki/Coefficient_of_variation for details.

Definition at line 1125 of file statistics.hpp.

coefficient_of_variation() [2/2]

std::vector<double> genesis::utils::coefficient_of_variation ( std::vector< MeanStddevPair > const &  ms )

inline

Calculate the index of dispersion.

The coefficient of variation (CV), also known as the relative standard deviation (RSD), is defined as the ratio of the standard deviation to the mean. See mean_stddev() to calculate those values. See https://en.wikipedia.org/wiki/Coefficient_of_variation for details.

Definition at line 1133 of file statistics.hpp.

color_from_bytes()

Color color_from_bytes	(	unsigned char	r,
		unsigned char	g,
		unsigned char	b,
		unsigned char	a
	)

Create a Color given three or four values in the range [ 0, 255 ] for each of the components red, green and blue, and optionally alpha.

Definition at line 53 of file utils/color/functions.cpp.

color_from_hex()

Color color_from_hex	(	std::string const &	hex_color,
		std::string const &	prefix = "#"
	)

Create a Color given a hex color string in the format "#003366[ff]".

The hash sign in the beginning can be replaced by any given prefix. If the string is not correctly formatted, an std::invalid_argument exception is thrown. If the string contains only RGB, alpha is set to 1.0.

Definition at line 63 of file utils/color/functions.cpp.

color_from_name()

Color color_from_name

(

std::string const &

name

)

Return the color represented by the given name, which is (currently) a shortcut for color_from_name_web() and color_from_name_xkcd().

Definition at line 1518 of file names.cpp.

color_from_name_lego()

Color color_from_name_lego

(

std::string const &

name

)

Retrieve a named LEGO color by name.

Names are compared only by their alnum chars, and the letter case is ignored. If the color name does not exist, an std::invalid_argument exception is thrown.

The colors are taken from the colors.csv.gz table of the LEGO Catalog Database at https://rebrickable.com/downloads/ on 2024-06-17. They were published with the note

You can use these files for any purpose.

which we interpret as the table being in the public domain.

Definition at line 1592 of file names.cpp.

color_from_name_web()

Color color_from_name_web

(

std::string const &

name

)

Retrieve a named web color by name.

Names are compared only by their alnum chars, and the letter case is ignored. If the color name does not exist, an std::invalid_argument exception is thrown.

Definition at line 1542 of file names.cpp.

color_from_name_xkcd()

Color color_from_name_xkcd

(

std::string const &

name

)

Retrieve a named xkcd color by name.

Names are compared only by their alnum chars, and the letter case is ignored. If the color name does not exist, an std::invalid_argument exception is thrown.

The colors are taken from an [https://xkcd.com/](xkcd) color survey. They were published under Public Domain, http://creativecommons.org/publicdomain/zero/1.0/. See https://xkcd.com/color/rgb/ and https://blog.xkcd.com/2010/05/03/color-survey-results/ for details. See also our Acknowledgements.

Definition at line 1567 of file names.cpp.

color_list_accent()

std::vector< Color > const & color_list_accent

(

)

Color palette accent.

Provides a color palette with 8 colors, 4 pale and 4 saturated, for use with qualitative/categorical data.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 158 of file list_qualitative.cpp.

color_list_blues()

std::vector< Color > const & color_list_blues

(

)

Color palette blues.

Provides a sequential blue color palette of increasing saturation.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 1411 of file list_sequential.cpp.

color_list_brbg()

std::vector< Color > const & color_list_brbg

(

)

Color palette brbg.

Provides a diverging color palette with brown low, white middle, and blue-green high.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 200 of file list_diverging.cpp.

color_list_bugn()

std::vector< Color > const & color_list_bugn

(

)

Color palette bugn.

Provides a sequential blue-green color palette of increasing saturation.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 1416 of file list_sequential.cpp.

color_list_bupu()

std::vector< Color > const & color_list_bupu

(

)

Color palette bupu.

Provides a sequential blue-purple color palette of increasing saturation.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 1421 of file list_sequential.cpp.

color_list_bupubk()

std::vector< Color > const & color_list_bupubk

(

)

Color Palette bupubk.

Provides a sequential blue color palette of light blue, purple and black. Particularly useful for visualizing trees, as the light blue is still visible when used to color branches.

Definition at line 1406 of file list_sequential.cpp.

color_list_dark2()

std::vector< Color > const & color_list_dark2

(

)

Color palette dark2.

Provides a color palette with 8 dark colors based on color_list_set2() for use with qualitative/categorical data.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 163 of file list_qualitative.cpp.

color_list_diverging() [1/2]

std::vector< Color > const & color_list_diverging

(

ColorListDiverging

palette

)

Definition at line 249 of file list_diverging.cpp.

color_list_diverging() [2/2]

std::vector< Color > const & color_list_diverging

(

std::string const &

palette

)

Definition at line 282 of file list_diverging.cpp.

color_list_diverging_names()

std::vector< std::string > color_list_diverging_names

(

)

Definition at line 317 of file list_diverging.cpp.

color_list_gnbu()

std::vector< Color > const & color_list_gnbu

(

)

Color palette gnbu.

Provides a sequential green-blue color palette of increasing saturation.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 1426 of file list_sequential.cpp.

color_list_greens()

std::vector< Color > const & color_list_greens

(

)

Color palette greens.

Provides a sequential green color palette of increasing saturation.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 1431 of file list_sequential.cpp.

color_list_greys()

std::vector< Color > const & color_list_greys

(

)

Color palette greys.

Provides a sequential grey color palette of increasing saturation.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 1436 of file list_sequential.cpp.

color_list_heat()

std::vector< Color > const & color_list_heat

(

)

Color palette heat.

Provides a sequential heat color palette from white via yellow to orange and red.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 1501 of file list_sequential.cpp.

color_list_inferno()

std::vector< Color > const & color_list_inferno

(

)

Color palette inferno.

This Matplotlib color palette is adapted from https://github.com/BIDS/colormap. New matplotlib colormaps by Nathaniel J. Smith, Stefan van der Walt, and Eric Firing. The colormaps are released under the CC0 license / public domain dedication. See https://creativecommons.org/publicdomain/zero/1.0/ for the license. See also our Acknowledgements.

Definition at line 1511 of file list_sequential.cpp.

color_list_magma()

std::vector< Color > const & color_list_magma

(

)

Color palette magma.

This Matplotlib color palette is adapted from https://github.com/BIDS/colormap. New matplotlib colormaps by Nathaniel J. Smith, Stefan van der Walt, and Eric Firing. The colormaps are released under the CC0 license / public domain dedication. See https://creativecommons.org/publicdomain/zero/1.0/ for the license. See also our Acknowledgements.

Definition at line 1506 of file list_sequential.cpp.

color_list_misc() [1/2]

std::vector< Color > const & color_list_misc

(

ColorListMisc

palette

)

Definition at line 480 of file list_misc.cpp.

color_list_misc() [2/2]

std::vector< Color > const & color_list_misc

(

std::string const &

palette

)

Definition at line 489 of file list_misc.cpp.

color_list_misc_names()

std::vector< std::string > color_list_misc_names

(

)

Definition at line 500 of file list_misc.cpp.

color_list_nextstrain() [1/2]

std::vector< Color > const & color_list_nextstrain

(

)

Color palette from the the Nextstrain build for novel coronavirus (nCoV) at https://nextstrain.org/ncov.

The palette starts at purple and blue, progresses via green and yellow, towards orange and red. This function returns a palette with 256 entries. The original palette also has a reduced set of colors when using < 16 entries. We made these available via the color_list_nextstrain( size_t n ) function, see there for details.

This color palette is adapted from the Nextstrain build for novel coronavirus (nCoV) at https://nextstrain.org/ncov, using their color scheme https://github.com/nextstrain/ncov/blob/master/config/color_schemes.tsv and converting parts of it to RGB double values. The repository at https://github.com/nextstrain/ncov is published under the MIT license. See also our Acknowledgements.

Definition at line 471 of file list_misc.cpp.

color_list_nextstrain() [2/2]

std::vector< Color > color_list_nextstrain

(

size_t

n

)

Color palette from the the Nextstrain build for novel coronavirus (nCoV) at https://nextstrain.org/ncov.

The original palette has a reduced set of colors when using < 16 entries. This function makes these reduced color sets available when using n < 16. All values above that use the full palette (with 256) and interpolate to the requested number of entries. NB: The original palette continues to 500 colors as well, but the differences between adjacent entries are diminishing, so that our approach of interpolation when requesting a palette with more than 256 entries yields highly similar entries. Also, who needs a palette with that many entries anyway?!

This color palette is adapted from the Nextstrain build for novel coronavirus (nCoV) at https://nextstrain.org/ncov, using their color scheme https://github.com/nextstrain/ncov/blob/master/config/color_schemes.tsv and converting parts of it to RGB double values. The repository at https://github.com/nextstrain/ncov is published under the MIT license. See also our Acknowledgements.

Definition at line 460 of file list_misc.cpp.

color_list_oranges()

std::vector< Color > const & color_list_oranges

(

)

Color palette oranges.

Provides a sequential orange color palette of increasing saturation.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 1441 of file list_sequential.cpp.

color_list_orrd()

std::vector< Color > const & color_list_orrd

(

)

Color palette orrd.

Provides a sequential orange-red color palette of increasing saturation.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 1446 of file list_sequential.cpp.

color_list_paired()

std::vector< Color > const & color_list_paired

(

)

Color palette paired.

Provides a color palette with 12 colors in 6 pairs for use with qualitative/categorical data.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 168 of file list_qualitative.cpp.

color_list_pastel1()

std::vector< Color > const & color_list_pastel1

(

)

Color palette pastel1.

Provides a color palette with 9 colors based on color_list_set1() for use with qualitative/categorical data.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 173 of file list_qualitative.cpp.

color_list_pastel2()

std::vector< Color > const & color_list_pastel2

(

)

Color palette pastel2.

Provides a color palette with 9 colors based on color_list_set2() for use with qualitative/categorical data.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 178 of file list_qualitative.cpp.

color_list_piyg()

std::vector< Color > const & color_list_piyg

(

)

Color palette piyg.

Provides a diverging color palette with pink low, white middle, and yellow-green high.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 205 of file list_diverging.cpp.

color_list_plasma()

std::vector< Color > const & color_list_plasma

(

)

Color palette plasma.

This Matplotlib color palette is adapted from https://github.com/BIDS/colormap. New matplotlib colormaps by Nathaniel J. Smith, Stefan van der Walt, and Eric Firing. The colormaps are released under the CC0 license / public domain dedication. See https://creativecommons.org/publicdomain/zero/1.0/ for the license. See also our Acknowledgements.

Definition at line 1516 of file list_sequential.cpp.

color_list_prgn()

std::vector< Color > const & color_list_prgn

(

)

Color palette prgn.

Provides a diverging color palette with purple low, white middle, and green high.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 210 of file list_diverging.cpp.

color_list_pubu()

std::vector< Color > const & color_list_pubu

(

)

Color palette pubu.

Provides a sequential purple-blue color palette of increasing saturation.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 1451 of file list_sequential.cpp.

color_list_pubugn()

std::vector< Color > const & color_list_pubugn

(

)

Color palette pubugn.

Provides a sequential purple-blue-green color palette of increasing saturation.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 1456 of file list_sequential.cpp.

color_list_puor()

std::vector< Color > const & color_list_puor

(

)

Color palette puor.

Provides a diverging color palette with orange low, white middle, and purple high.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 215 of file list_diverging.cpp.

color_list_purd()

std::vector< Color > const & color_list_purd

(

)

Color palette purd.

Provides a sequential purple-red color palette of increasing saturation.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 1461 of file list_sequential.cpp.

color_list_purples()

std::vector< Color > const & color_list_purples

(

)

Color palette purples.

Provides a sequential purple color palette of increasing saturation.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 1466 of file list_sequential.cpp.

color_list_qualitative() [1/2]

std::vector< Color > const & color_list_qualitative

(

ColorListQualitative

palette

)

Definition at line 202 of file list_qualitative.cpp.

color_list_qualitative() [2/2]

std::vector< Color > const & color_list_qualitative

(

std::string const &

palette

)

Definition at line 232 of file list_qualitative.cpp.

color_list_qualitative_names()

std::vector< std::string > color_list_qualitative_names

(

)

Definition at line 264 of file list_qualitative.cpp.

color_list_rdbu()

std::vector< Color > const & color_list_rdbu

(

)

Color palette rdbu.

Provides a diverging color palette with red low, white middle, and blue high.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 220 of file list_diverging.cpp.

color_list_rdgy()

std::vector< Color > const & color_list_rdgy

(

)

Color palette rdgy.

Provides a diverging color palette with red low, white middle, and grey high.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 225 of file list_diverging.cpp.

color_list_rdpu()

std::vector< Color > const & color_list_rdpu

(

)

Color palette rdpu.

Provides a sequential red-purple color palette of increasing saturation.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 1471 of file list_sequential.cpp.

color_list_rdylbu()

std::vector< Color > const & color_list_rdylbu

(

)

Color palette rdylbu.

Provides a diverging color palette with red low, pale yellow middle, and blue high.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 230 of file list_diverging.cpp.

color_list_rdylgn()

std::vector< Color > const & color_list_rdylgn

(

)

Color palette rdylgn.

Provides a diverging color palette with red low, pale yellow middle, and green high.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 235 of file list_diverging.cpp.

color_list_reds()

std::vector< Color > const & color_list_reds

(

)

Color palette reds.

Provides a sequential red color palette of increasing saturation.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 1476 of file list_sequential.cpp.

color_list_sequential() [1/2]

std::vector< Color > const & color_list_sequential

(

ColorListSequential

palette

)

Definition at line 1530 of file list_sequential.cpp.

color_list_sequential() [2/2]

std::vector< Color > const & color_list_sequential

(

std::string const &

palette

)

Definition at line 1608 of file list_sequential.cpp.

color_list_sequential_names()

std::vector< std::string > color_list_sequential_names

(

)

Definition at line 1688 of file list_sequential.cpp.

color_list_set1()

std::vector< Color > const & color_list_set1

(

)

Color palette set1.

Provides a color palette with 9 easy-to-name colors for use with qualitative/categorical data.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 183 of file list_qualitative.cpp.

color_list_set2()

std::vector< Color > const & color_list_set2

(

)

Color palette set2.

Provides a color palette with 8 hard-to-name colors for use with qualitative/categorical data.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 188 of file list_qualitative.cpp.

color_list_set3()

std::vector< Color > const & color_list_set3

(

)

Color palette set3.

Provides a color palette with 12 colors for use with qualitative/categorical data. The colors are more saturated than the Pastels but less so than set2().

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 193 of file list_qualitative.cpp.

color_list_spectral()

std::vector< Color > const & color_list_spectral

(

)

Color palette spectral.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 240 of file list_diverging.cpp.

color_list_viridis()

std::vector< Color > const & color_list_viridis

(

)

Color palette viridis.

This Matplotlib color palette is adapted from https://github.com/BIDS/colormap. New matplotlib colormaps by Nathaniel J. Smith, Stefan van der Walt, and Eric Firing. The colormaps are released under the CC0 license / public domain dedication. See https://creativecommons.org/publicdomain/zero/1.0/ for the license. See also our Acknowledgements.

Definition at line 1521 of file list_sequential.cpp.

color_list_ylgn()

std::vector< Color > const & color_list_ylgn

(

)

Color palette ylgn.

Provides a sequential yellow-green color palette of increasing saturation.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 1481 of file list_sequential.cpp.

color_list_ylgnbu()

std::vector< Color > const & color_list_ylgnbu

(

)

Color palette ylgnbu.

Provides a sequential yellow-green-blue color palette of increasing saturation.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 1486 of file list_sequential.cpp.

color_list_ylorbr()

std::vector< Color > const & color_list_ylorbr

(

)

Color palette ylorbr.

Provides a sequential yellow-orange-brown color palette of increasing saturation.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 1491 of file list_sequential.cpp.

color_list_ylorrd()

std::vector< Color > const & color_list_ylorrd

(

)

Color palette ylorrd.

Provides a sequential yellow-orange-red color palette of increasing saturation.

Provides a diverging rainbow color palette with red low, pale yellow middle, and blue high.

This ColorBrewer color palette is adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the colors to RGB double values. The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider, and published under the Apache-2.0 license. See also our Acknowledgements.

Definition at line 1496 of file list_sequential.cpp.

color_palette_lego()

std::vector< Color > color_palette_lego

(

)

Definition at line 1603 of file names.cpp.

color_palette_web()

std::vector< Color > color_palette_web

(

)

Definition at line 1553 of file names.cpp.

color_palette_xkcd()

std::vector< Color > color_palette_xkcd

(

)

Definition at line 1578 of file names.cpp.

color_stops() [1/5]

std::map< double, Color > color_stops	(	ColorMap const &	map,
		ColorNormalization const &	norm
	)

Definition at line 53 of file helpers.cpp.

color_stops() [2/5]

std::map< double, Color > color_stops	(	ColorMap const &	map,
		ColorNormalizationBoundary const &	norm
	)

Definition at line 138 of file helpers.cpp.

color_stops() [3/5]

std::map< double, Color > color_stops	(	ColorMap const &	map,
		ColorNormalizationDiverging const &	norm
	)

Definition at line 94 of file helpers.cpp.

color_stops() [4/5]

std::map< double, Color > color_stops	(	ColorMap const &	map,
		ColorNormalizationLinear const &	norm
	)

Definition at line 78 of file helpers.cpp.

color_stops() [5/5]

std::map< double, Color > color_stops	(	ColorMap const &	map,
		ColorNormalizationLogarithmic const &	norm
	)

Definition at line 89 of file helpers.cpp.

color_tickmarks() [1/5]

std::map< double, std::string > color_tickmarks	(	ColorNormalization const &	norm,
		size_t	num_ticks
	)

Definition at line 157 of file helpers.cpp.

color_tickmarks() [2/5]

std::map< double, std::string > color_tickmarks	(	ColorNormalizationBoundary const &	norm,
		size_t	num_ticks
	)

Definition at line 262 of file helpers.cpp.

color_tickmarks() [3/5]

std::map< double, std::string > color_tickmarks	(	ColorNormalizationDiverging const &	norm,
		size_t	num_ticks
	)

Definition at line 215 of file helpers.cpp.

color_tickmarks() [4/5]

std::map< double, std::string > color_tickmarks	(	ColorNormalizationLinear const &	norm,
		size_t	num_ticks
	)

Definition at line 182 of file helpers.cpp.

color_tickmarks() [5/5]

std::map< double, std::string > color_tickmarks	(	ColorNormalizationLogarithmic const &	norm,
		size_t	num_ticks
	)

Definition at line 193 of file helpers.cpp.

color_to_hex()

std::string color_to_hex	(	Color const &	c,
		std::string const &	prefix = "#",
		bool	uppercase = false,
		bool	with_alpha = false
	)

Return a hex string representation of a Color in the format "#003366[ff]".

The hash sign in the beginning can be replaced by any given prefix. If uppercase is set to true, any outputted alphabetical chars (that is, A to F for hex strings) are uppercase. if with_alpha is set to true, two additional hex digits are printed for the alpha channel.

Definition at line 100 of file utils/color/functions.cpp.

combine_hashes()

constexpr std::size_t genesis::utils::combine_hashes ( std::size_t  h1, std::size_t  h2  )

inlineconstexpr

Combine two hash values.

Definition at line 127 of file std.hpp.

combine_hashes_32()

constexpr std::size_t genesis::utils::combine_hashes_32 ( std::size_t  h1, std::size_t  h2  )

inlineconstexpr

Definition at line 114 of file std.hpp.

combine_hashes_64()

constexpr std::size_t genesis::utils::combine_hashes_64 ( std::size_t  h1, std::size_t  h2  )

inlineconstexpr

Definition at line 119 of file std.hpp.

compare_natural()

int compare_natural	(	std::string const &	lhs,
		std::string const &	rhs
	)

Compare two strings with natural human sorting, that is "A1", "A2", "A100", instead of the standard sort by ASCII value "A1", "A100", "A2".

Returns negavie if lhs < rhs, 0 if they are equal, and positive if lhs > rhs.

Definition at line 341 of file string.cpp.

compare_threeway()

constexpr int genesis::utils::compare_threeway ( T  lhs, U  rhs  )

inlineconstexpr

Three-way comparison (spaceship operator) for C++ <20.

Return -1 if lhs < rhs, return +1 if lhs > rhs, return 0 if lhs == rhs, for arithmetic types.

Definition at line 145 of file common.hpp.

contains()

bool genesis::utils::contains ( const C &  v, const T &  x  )

inline

Returns whether a container object has a certain element.

The usage of std::find just to check for presence of a certain item is a bit cumbersome. This template simply takes any container and a value and returns true iff the value is present in the container.

Definition at line 74 of file algorithm.hpp.

contains_ci()

bool contains_ci	(	std::vector< std::string > const &	haystack,
		std::string const &	needle
	)

Return whether a vector of strings contains a given string, case insensitive.

Definition at line 59 of file string.cpp.

contains_ci_alnum()

bool contains_ci_alnum	(	std::vector< std::string > const &	haystack,
		std::string const &	needle
	)

Return whether a vector of strings contains a given string, case insensitive, and ignoring all non-alphanumerical characters.

Definition at line 71 of file string.cpp.

contains_duplicates()

bool genesis::utils::contains_duplicates ( C const &  v )

inline

Return whether a container contains duplicates.

The container does not need to be sorted. For speed, the function internally copies the elements of the container.

Definition at line 86 of file algorithm.hpp.

convert_from_string()

T genesis::utils::convert_from_string	(	std::string const &	str,
		bool	trim = false
	)

Generic conversion from string to any data type that is supported by std::stringsteam operator >>.

This function is useful for general conversion. It throw when the string cannot be fully converted. That is, if there is more content after the converted value. If trim is false (default), this is also affected by white space. In that case, the value to be parsed has to be the only content of the input string.

Definition at line 59 of file convert.hpp.

convert_from_string< double >()

double genesis::utils::convert_from_string< double > ( std::string const &  str, bool  trim  )

inline

Specialization of the generic conversion function for double, which also takes nan and inf into account.

Definition at line 101 of file convert.hpp.

convert_from_string< std::string >()

std::string genesis::utils::convert_from_string< std::string > ( std::string const &  str, bool  trim  )

inline

Specialization of the generic conversion function for std::string.

Definition at line 89 of file convert.hpp.

convert_geo_coordinate() [1/2]

GeoCoordinate convert_geo_coordinate

(

std::string const &

coordinate

)

Parse a string of geographic coordinates.

The function accepts many different formats for geographical coordinates. Some exemplary valid cases:

• 50d4m17.698N 14d24m2.826E
• 40:26:46N,79:56:55W
• 40:26:46.302N 179:56:55.903W
• 49°59'56.948"N, 15°48'22.989"E
• 50d4m17.698N 14d24m2.826E
• 49.9991522N, 150.8063858E
• 40°26′47″N 79°58′36″W
• 40d 26′ 47″ N 79d 58′ 36″ W
• 40.446195N 79.948862W
• 40,446195° 79,948862°
• 40° 26.7717 / -79° 56.93172
• 40.446195, -79.948862
• N 49° 59.94913', E 15° 48.38315'

The hemispheres can be given as [NS] for the first component and [EW] for the second, and can either preceed or follow the numeric values. Degrees, Minutes and Seconds can be separated by the letters [dms], by degree (°), prime ( ′ ), single quotation mark (‘’), double prime (″), double quoation mark ("), or by colons (:), respectively. The two components (NS and EW) can be separated by comma (,) or slash (/`).

There are some caveats: The hemisphere strings (NESW) have to be in capitial letters, while the letters used for degrees, minute and seconds (dms) have to be lower case. This constraint avoids ambiguity between seconds (s) and south (S). Also, either the decimal separator can be a comma, or the separator between components, but not both. This again avoids ambiguity while parsing.

Definition at line 255 of file utils/tools/geodesy/functions.cpp.

convert_geo_coordinate() [2/2]

GeoCoordinate convert_geo_coordinate	(	std::string const &	latitude,
		std::string const &	longitude
	)

Parse strings of geographic coordinates.

This is the same as convert_geo_coordinate( std::string const& ), with the only different being that the two components (NW and EW) are given separately. See there for details.

Definition at line 250 of file utils/tools/geodesy/functions.cpp.

convert_single_geo_coordinate_()

static double genesis::utils::convert_single_geo_coordinate_ ( std::string const &  h1, std::string const &  d, std::string const &  m, std::string const &  s, std::string const &  h2, GeoCoordinateComponent  component  )

static

Local helper function that takes parts of the regex matches and converts them to double.

The strings h1, d, m, s and h2 are the matches of the regex. The parameter component is the hemisphere of this coordinate component, NS or EW, which is determined by whether the matches are the first or the second component of the coordinate.

Definition at line 70 of file utils/tools/geodesy/functions.cpp.

convert_to_bool() [1/5]

void convert_to_bool	(	Dataframe &	df,
		size_t	col_index
	)

Definition at line 156 of file utils/containers/dataframe/operators.cpp.

convert_to_bool() [2/5]

void convert_to_bool	(	Dataframe &	df,
		std::string const &	col_name
	)

Definition at line 186 of file utils/containers/dataframe/operators.cpp.

convert_to_bool() [3/5]

std::vector<bool> genesis::utils::convert_to_bool	(	ForwardIterator	first,
		ForwardIterator	last,
		size_t	size = 0
	)

Definition at line 144 of file convert.hpp.

convert_to_bool() [4/5]

bool convert_to_bool

(

std::string const &

str

)

Convert a string to bool, return the result, and throw an exception when the conversion was not successful.

Strings that can be converted to bool with this function are true, false, yes, no, on, off, 1, 0, and the empty string (evaluated as false), with all text case insensitive.

Definition at line 65 of file convert.cpp.

convert_to_bool() [5/5]

bool convert_to_bool	(	std::string const &	str,
		bool &	result
	)

Convert a string to bool, store the result in result, and return whether the conversion as successful.

Strings that can be converted to bool with this function are true, false, yes, no, on, off, 1, 0, and the empty string (evaluated as false), with all text case insensitive.

Definition at line 49 of file convert.cpp.

convert_to_bool_double() [1/3]

std::vector<double> genesis::utils::convert_to_bool_double	(	ForwardIterator	first,
		ForwardIterator	last,
		size_t	size = 0
	)

Definition at line 207 of file convert.hpp.

convert_to_bool_double() [2/3]

double convert_to_bool_double

(

std::string const &

str

)

Convert a string to bool, but return it as a double, and throw an exception when the conversion was not successful.

This conversion is useful to work with dataframes that are all double, for example to work with our Generalized Linear Model implementation, see glm_fit().

Strings that can be converted to bool with this function are true, false, yes, no, on, off, 1, 0, and the empty string (evaluated as quiet_NaN), with all text case insensitive.

Definition at line 103 of file convert.cpp.

convert_to_bool_double() [3/3]

bool convert_to_bool_double	(	std::string const &	str,
		double &	result
	)

Convert a string to bool, but store the result as a double in result, and return whether the conversion as successful.

This conversion is useful to work with dataframes that are all double, for example to work with our Generalized Linear Model implementation, see glm_fit().

Strings that can be converted to bool with this function are true, false, yes, no, on, off, 1, 0, and the empty string (evaluated as quiet_NaN), with all text case insensitive.

Definition at line 84 of file convert.cpp.

convert_to_double() [1/5]

void convert_to_double	(	Dataframe &	df,
		size_t	col_index
	)

Definition at line 192 of file utils/containers/dataframe/operators.cpp.

convert_to_double() [2/5]

void convert_to_double	(	Dataframe &	df,
		std::string const &	col_name
	)

Definition at line 206 of file utils/containers/dataframe/operators.cpp.

convert_to_double() [3/5]

std::vector<double> genesis::utils::convert_to_double	(	ForwardIterator	first,
		ForwardIterator	last,
		size_t	size = 0
	)

Definition at line 260 of file convert.hpp.

convert_to_double() [4/5]

double convert_to_double

(

std::string const &

str

)

Convert a string to double, return the result, and throw an exception when the conversion was not successful.

Definition at line 161 of file convert.cpp.

convert_to_double() [5/5]

bool convert_to_double	(	std::string const &	str,
		double &	result
	)

Convert a string to double, store the result in result, and return whether the conversion as successful.

Definition at line 150 of file convert.cpp.

convert_to_numeric_()

bool genesis::utils::convert_to_numeric_	(	std::string const &	str,
		T &	result,
		T	initial,
		F	conversion
	)

Definition at line 123 of file convert.cpp.

convert_to_palette_()

static std::vector<Color> genesis::utils::convert_to_palette_ ( NamedColorList const &  list )

static

Local helper function to convert a list of byte colors into a proper Color vector.

Definition at line 1487 of file names.cpp.

convert_to_signed_integer() [1/3]

std::vector<long long> genesis::utils::convert_to_signed_integer	(	ForwardIterator	first,
		ForwardIterator	last,
		size_t	size = 0
	)

Definition at line 313 of file convert.hpp.

convert_to_signed_integer() [2/3]

long long convert_to_signed_integer

(

std::string const &

str

)

Convert a string to signed integer, return the result, and throw an exception when the conversion was not successful.

Definition at line 193 of file convert.cpp.

convert_to_signed_integer() [3/3]

bool convert_to_signed_integer	(	std::string const &	str,
		long long &	result
	)

Convert a string to signed integer, store the result in result, and return whether the conversion as successful.

Definition at line 182 of file convert.cpp.

convert_to_tm() [1/6]

std::vector<std::tm> genesis::utils::convert_to_tm	(	ForwardIterator	first,
		ForwardIterator	last,
		size_t	size = 0
	)

Convert a list of std::string to std::tm date/time objects, if possible. Throw otherwise.

The function tries to guess the format. See convert_to_tm( std::string const& ) for details. For long lists, this can be expensive, as the formats are tried again for each entry separately.

If the size of the list is known, this can be given to reserve that much memory first.

Definition at line 314 of file date_time.hpp.

convert_to_tm() [2/6]

std::vector<std::tm> genesis::utils::convert_to_tm	(	ForwardIterator	first,
		ForwardIterator	last,
		std::string const &	format,
		size_t	size = 0
	)

Convert a list of std::string to std::tm date/time objects, if possible. Throw otherwise.

The function uses the given format. See convert_to_tm( std::string const&, std::string const& ) for details.

If the size of the list is known, this can be given to reserve that much memory first.

Definition at line 287 of file date_time.hpp.

convert_to_tm() [3/6]

std::vector<std::tm> genesis::utils::convert_to_tm	(	ForwardIterator	first,
		ForwardIterator	last,
		std::string const &	format,
		std::string const &	locale,
		size_t	size = 0
	)

Convert a list of std::string to std::tm date/time objects, if possible. Throw otherwise.

The function uses the given format and locale. See convert_to_tm( std::string const&, std::string const&, std::string const& ) for details.

If the size of the list is known, this can be given to reserve that much memory first.

Definition at line 260 of file date_time.hpp.

convert_to_tm() [4/6]

std::tm convert_to_tm

(

std::string const &

str

)

Convert a std::string to a std::tm date/time object, if possible. Throw otherwise.

The function tries different common formats for convenience, in the following order: First only dates, then dates/times combined, last only times. The reasoning for that order is that in most typical scientific datasets, the day is more relevant than the exact time during the day, so they mostly likely contain dates only.

The exact formats that are tried are as follows:

#	Format	Type	Explanation	Example
1	%Y-%m-%d	Date	ISO 8601 extended format	2020-04-17
2	%Y%m%d	Date	ISO 8601 basic format	20200417
3	%Y-%m-%dT%H:%M:%S	Date/Time	ISO 8601 extended format	2020-04-17T00:27:58
4	%Y-%m-%d %H:%M:%S	Date/Time	ISO 8601 extended format, but separated by a whitespace, as allowed in RFC 3339	2020-04-17 00:27:58
5	%Y%m%dT%H%M%S	Date/Time	ISO 8601 basic format	20200417T002758
6	%Y%m%d %H%M%S	Date/Time	ISO 8601 basic format, but separated by a whitespace	20200417 002758
7	%Y%m%d%H%M%S	Date/Time	ISO 8601 basic format, with no separator	20200417002758
8	%H:%M:%S	Time	ISO 8601 extended format	00:27:58
9	%H%M%S	Time	ISO 8601 basic format	002758

While this will most likely be able to parse any given date/time string that is used in scientific data, it is almost certainly slower than setting the format manually, if known, using the function convert_to_tm( std::string const&, std::string const& )

More exotic formats, such as the stupid US format 04/17/2020, or the slighly more reasonable UK format 17/04/2020, are not tried, as they might be mistaken for one another. Furthermore, time zone information is not used and leads to an exception being thrown (e.g., "2020-04-06T00:27:58+00:00" or "20200406T002758Z"). If those are needed, they have to be specified, again using the function convert_to_tm( std::string const&, std::string const& )

Definition at line 341 of file date_time.cpp.

convert_to_tm() [5/6]

std::tm convert_to_tm	(	std::string const &	str,
		std::string const &	format
	)

Convert a std::string to a std::tm date/time object, if possible. Throw otherwise.

For a list of the available format parameters, see https://en.cppreference.com/w/cpp/io/manip/get_time or http://www.cplusplus.com/reference/ctime/strftime/

The function tries different std::locale settings for convenience, in the order "C" (POSIX), "en_US.UTF-8", and "" (user-preferred). If a format is used that does not depend on the locale, this does not induce a performance penalty. In order to also specify the locale, use convert_to_tm( std::string const&, std::string const&, std::string const& ) instead.

Definition at line 325 of file date_time.cpp.

convert_to_tm() [6/6]

std::tm convert_to_tm	(	std::string const &	str,
		std::string const &	format,
		std::string const &	locale
	)

Convert a std::string to a std::tm date/time object, if possible. Throw otherwise.

For a list of the available format parameters, see https://en.cppreference.com/w/cpp/io/manip/get_time or http://www.cplusplus.com/reference/ctime/strftime/

The available locale strings depend on the operating system and user settings. Typically, on Unix/Linux/POSIX/MacOS machines, the command locale -a should give a valid list.

Definition at line 314 of file date_time.cpp.

convert_to_tm_()

bool genesis::utils::convert_to_tm_	(	std::string const &	str,
		std::string const &	format,
		std::string const &	locale,
		std::tm &	t
	)

Local helper function that does the heavy load of time conversion.

We use this variant, which returns its success, to not have to try catch in the functions that guess the format.

Definition at line 242 of file date_time.cpp.

convert_to_type_() [1/2]

void genesis::utils::convert_to_type_	(	Dataframe &	df,
		size_t	col_index
	)

Definition at line 111 of file utils/containers/dataframe/operators.cpp.

convert_to_type_() [2/2]

void genesis::utils::convert_to_type_	(	Dataframe &	df,
		size_t	col_index
	)

Definition at line 123 of file utils/containers/dataframe/operators.cpp.

convert_to_unsigned_integer() [1/3]

std::vector<unsigned long long> genesis::utils::convert_to_unsigned_integer	(	ForwardIterator	first,
		ForwardIterator	last,
		size_t	size = 0
	)

Definition at line 366 of file convert.hpp.

convert_to_unsigned_integer() [2/3]

unsigned long long convert_to_unsigned_integer

(

std::string const &

str

)

Convert a string to unsigned integer, return the result, and throw an exception when the conversion was not successful.

Definition at line 225 of file convert.cpp.

convert_to_unsigned_integer() [3/3]

bool convert_to_unsigned_integer	(	std::string const &	str,
		unsigned long long &	result
	)

Convert a string to unsigned integer, store the result in result, and return whether the conversion as successful.

Definition at line 214 of file convert.cpp.

correlation_matrix()

Matrix< double > correlation_matrix

(

Matrix< double > const &

data

)

Calculate the correlation Matrix of a given data Matrix.

This is done by standardizing the mean and variance of the given data and then calculating the sums_of_squares_and_cross_products_matrix().

Definition at line 197 of file math/matrix.cpp.

count_finite_elements()

std::pair<size_t, size_t> genesis::utils::count_finite_elements	(	ForwardIterator	first,
		ForwardIterator	last
	)

Count the number of finite elements in a range of double values.

The function iterates a range of values that are expected to be double values. It uses std::isfinite as criterion for validity of the values.

The return value is a pair containing the number of finite elements as first, and the number of total number elements in the range as second (the size of the range).

Definition at line 150 of file statistics.hpp.

count_substring_occurrences()

size_t count_substring_occurrences	(	std::string const &	str,
		std::string const &	sub
	)

Return the number of (possibly overlapping) occurrences of a substring in a string.

Definition at line 518 of file string.cpp.

covariance_matrix()

Matrix< double > covariance_matrix

(

Matrix< double > const &

data

)

Calculate the covariance Matrix of a given data Matrix.

This is done by standardizing the mean of the given data and then calculating the sums_of_squares_and_cross_products_matrix().

Definition at line 211 of file math/matrix.cpp.

cubed()

constexpr double genesis::utils::cubed ( double  x )

inlineconstexpr

Cube of a number.

Simply \( x^3 \), but faster than std::pow for the low exponent. Meant as an abbreviation where the argument is not already a variable, e.g., cubed( x - 1.0 ), without the need to store the intermediate argument term.

Definition at line 235 of file common.hpp.

current_date()

std::string current_date

(

)

Returns the current date as a string in the format "2014-12-31".

Definition at line 68 of file date_time.cpp.

current_path()

std::string current_path

(

)

Return the current (working) directory, simiar to getcwd().

The function behaves similar to getcwd(). The path is returned with a trailing slash, for conveniently apppending file names to it.

As this function changes the directory in the process, it is not thread safe.

Definition at line 502 of file fs.cpp.

current_path_getcwd_()

static std::string genesis::utils::current_path_getcwd_ ( )

static

Definition at line 361 of file fs.cpp.

current_path_unix_()

static std::string genesis::utils::current_path_unix_ ( )

static

Definition at line 392 of file fs.cpp.

current_time()

std::string current_time

(

)

Returns the current time as a string in the format "13:37:42".

Definition at line 88 of file date_time.cpp.

deescape() [1/2]

char deescape

(

char

c

)

Return the de-escaped char for a backslash-escaped char.

The function takes the char that follows a backslash in an escaped string and returns its de-escaped char. That is, n is turned into a new line (\n), t is turned into a tab (\t) and r is turned into a carrier return (\r). All other chars (e.g., quotation marks or the backslash itself) are simply returned as-is.

Definition at line 980 of file string.cpp.

deescape() [2/2]

std::string deescape

(

std::string const &

text

)

Return a string where backslash-escaped characters are transformed into their respective string form.

All occurrences of backslash + char in the string are de-escaped. That is, all \n, \t and \r are turned into their respective control sequences, while all other chars folloing a backslash are translated into the char itself (so that e.g., quotation marks or backslashes themself can be escaped).

Also see deescape( char c ).

Definition at line 958 of file string.cpp.

descending()

void genesis::utils::descending ( T &  f, T &  s  )

inline

Sort two values in descending order, inplace.

Definition at line 81 of file common.hpp.

detect_OS_AVX512_()

bool genesis::utils::detect_OS_AVX512_

(

)

Definition at line 553 of file info.cpp.

detect_OS_AVX_()

bool genesis::utils::detect_OS_AVX_

(

)

Definition at line 533 of file info.cpp.

detect_OS_x64_()

bool genesis::utils::detect_OS_x64_

(

)

Definition at line 493 of file info.cpp.

dir_create()

void dir_create	(	std::string const &	path,
		bool	with_parents = true
	)

Create a directory.

If the directory already exists, nothing happens. If the path exists, but is not a directory, a std::runtime_error is thrown. If the creation fails for some other reason, also a std::runtime_error is thrown.

Definition at line 236 of file fs.cpp.

dir_exists()

bool dir_exists

(

std::string const &

dir

)

Return true iff the directory exists.

Definition at line 218 of file fs.cpp.

dir_list_contents()

std::vector< std::string > dir_list_contents	(	std::string const &	dir,
		bool	full_path = false,
		std::string const &	regex = ""
	)

Get a list of files and directories in a directory.

If full_path is set to true, the path of the provided dir is prepended to the resulting list. If a non-empy regex is provided, file names are filtered by this regular expression.

If the directory is not readable, the function throws std::runtime_error.

Definition at line 318 of file fs.cpp.

dir_list_contents_()

static std::vector<std::string> genesis::utils::dir_list_contents_ ( std::string const &  dir, bool  full_path, std::string const &  regex, std::function< bool(std::string const &)>  condition  )

static

Definition at line 274 of file fs.cpp.

dir_list_directories()

std::vector< std::string > dir_list_directories	(	std::string const &	dir,
		bool	full_path = false,
		std::string const &	regex = ""
	)

Get a list of directories in a directory.

Behaves the same as dir_list_contents(), except tat only directories are listed (i.e., no files). See there for an explanation of the arguments.

Definition at line 347 of file fs.cpp.

dir_list_files()

std::vector< std::string > dir_list_files	(	std::string const &	dir,
		bool	full_path = false,
		std::string const &	regex = ""
	)

Get a list of files in a directory.

Behaves the same as dir_list_contents(), except tat only files are listed (i.e., no directories). See there for an explanation of the arguments.

Definition at line 329 of file fs.cpp.

dir_normalize_path()

std::string dir_normalize_path

(

std::string const &

path

)

Normalize a dir name, i.e., make sure that the given path ends with exaclty one slash.

Definition at line 269 of file fs.cpp.

double_frame()

TableLayout double_frame

(

bool

condensed

)

Definition at line 573 of file utils/text/table.cpp.

double_grid()

TableLayout double_grid

(

bool

condensed

)

Definition at line 554 of file utils/text/table.cpp.

earth_movers_distance()

double earth_movers_distance	(	const Histogram &	h1,
		const Histogram &	h2,
		bool	norm
	)

Definition at line 48 of file utils/math/histogram/distances.cpp.

ends_with() [1/2]

bool ends_with	(	std::string const &	text,
		std::string const &	suffix
	)

Return whether a string ends with another string, i.e., check for a suffix.

Definition at line 230 of file string.cpp.

ends_with() [2/2]

bool ends_with	(	std::string const &	text,
		std::string const &	suffix,
		std::string &	prefix
	)

Return whether a string ends with another string, i.e., check for a suffix.

This version of the function then stores the prefix of the matched text, containing all leading characters that did not match the suffix pattern. If there is no match, the prefix is left unchanged.

Definition at line 238 of file string.cpp.

ends_with_ci() [1/2]

bool ends_with_ci	(	std::string const &	text,
		std::string const &	suffix
	)

Return whether a string ends with another string, i.e., check for a suffix, case insensitive.

Definition at line 248 of file string.cpp.

ends_with_ci() [2/2]

bool ends_with_ci	(	std::string const &	text,
		std::string const &	suffix,
		std::string &	prefix
	)

Return whether a string ends with another string, i.e., check for a suffix, case insensitive.

This version of the function then stores the prefix of the matched text, containing all leading characters that did not match the suffix pattern. If there is no match, the prefix is left unchanged.

Definition at line 254 of file string.cpp.

ends_with_ci_alnum() [1/2]

bool ends_with_ci_alnum	(	std::string const &	text,
		std::string const &	suffix
	)

Return whether a string ends with another string (suffix), comparing case-independent, and ignoring all non-alphanumerical characters.

For example, "S2-1.sorted:1.REF_CNT" ends with "[ref-cnt]", according to this function.

Definition at line 264 of file string.cpp.

ends_with_ci_alnum() [2/2]

bool ends_with_ci_alnum	(	std::string const &	text,
		std::string const &	suffix,
		std::string &	prefix,
		bool	trim_prefix = false
	)

Return whether a string ends with another string (suffix), comparing case-independent, and ignoring all non-alphanumerical characters.

For example, "S2-1.sorted:1.REF_CNT" ends with "[ref-cnt]", according to this function.

This version of the function then stores the prefix of the matched text, containing all leading characters that did not match the suffix pattern. If there is no match, the prefix is left unchanged.

If additionally trim_prefix is set, all trailing non-alphanumerical characters of the prefix are removed. For example, "S2-1.sorted:1.REF_CNT" ends with "[ref-cnt]", and then contains the prefix "S2-1.sorted:1." - with trim_prefix, this is reduced to "S2-1.sorted:1" instead.

Definition at line 271 of file string.cpp.

equal_ranges()

bool equal_ranges	(	Histogram const &	lhs,
		Histogram const &	rhs
	)

Definition at line 55 of file histogram.cpp.

equals_ci()

bool equals_ci	(	std::string const &	lhs,
		std::string const &	rhs
	)

Compare two strings, case insensitive.

Definition at line 114 of file string.cpp.

equals_ci_alnum()

bool equals_ci_alnum	(	std::string const &	lhs,
		std::string const &	rhs
	)

Compare two strings, case insensitive, and ignoring all non-alphanumerical characters.

Definition at line 128 of file string.cpp.

erase_if()

void genesis::utils::erase_if ( Container &  c, UnaryPredicate  p  )

inline

Erases all elements from the container that satisfy a given predicate. An element is erased, if the predicate evaluates to true for it. The predicate needs to have a signature similar to (T const&)->bool.

Parameters

c	The container to modify.
p	The predicate to satisfy.

Definition at line 107 of file algorithm.hpp.

escape()

std::string escape

(

std::string const &

text

)

Return a string where special chars are replaces by their escape sequence.

All new lines are transformed into either \r or \n, tabs into \t. Double quotation marks are preceeded by a backslash, also the backslash itself will be escaped, so that "</tt> becomes <tt>\\" and \ becomes \\.

Definition at line 930 of file string.cpp.

euclidean_distance() [1/2]

double genesis::utils::euclidean_distance	(	ForwardIteratorA	first_a,
		ForwardIteratorA	last_a,
		ForwardIteratorB	first_b,
		ForwardIteratorB	last_b
	)

Calculate the Euclidean norm (L2 norm) distance between two (mathematical) vectors.

The function is a more expressive version of p_norm_distance( ForwardIteratorA, ForwardIteratorA, ForwardIteratorB, ForwardIteratorB, double ) with p == 2.0. See there for details.

Definition at line 381 of file distance.hpp.

euclidean_distance() [2/2]

double genesis::utils::euclidean_distance ( std::vector< double > const &  vec_a, std::vector< double > const &  vec_b  )

inline

Calculate the Euclidean norm (L2 norm) distance between two vectors of double elements.

The function is a more expressive version of p_norm_distance( std::vector<double> const&, std::vector<double> const&, double ) with p == 2.0. See there for details.

Definition at line 395 of file distance.hpp.

euclidean_distance_matrix()

Matrix< double > eucl