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 > euclidean_distance_matrix

(

Matrix< double > const &

data

)

Calculate the pairwise euclidean distance matrix between the rows of a given matrix.

See p_norm_distance_matrix() for details. This function simply uses a fixed p == 2.0 for more expressive code.

Definition at line 110 of file distance.cpp.

euclidean_norm() [1/2]

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

Calculate the Euclidean norm (L2 norm) of a range of numbers.

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

Definition at line 154 of file distance.hpp.

euclidean_norm() [2/2]

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

inline

Calculate the Euclidean norm (L2 norm) of a std::vector of double elements.

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

Definition at line 165 of file distance.hpp.

extended_frame()

TableLayout extended_frame

(

bool

condensed

)

Definition at line 523 of file utils/text/table.cpp.

extended_grid()

TableLayout extended_grid

(

bool

condensed

)

Definition at line 504 of file utils/text/table.cpp.

file_append()

void file_append	(	std::string const &	content,
		std::string const &	filename,
		bool	create_dirs = true
	)

Append the content of a string to a file.

If the file is not writable, the function throws std::runtime_error.

Definition at line 190 of file fs.cpp.

file_basename() [1/2]

std::string file_basename

(

std::string const &

filename

)

Remove directory name from file name if present.

Definition at line 788 of file fs.cpp.

file_basename() [2/2]

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.

After obtaining the file basename (the final rightmost segment of the file path after the last directory seperator /), the remove_extensions are also removed from the file name. The given list is iterated regularly, and removed (from right to left, as these are suffixes) from the file name, if present.

For example:

std::string path = "/path/to/filename.txt.gz";
std::cout << file_basename( path, { ".gz", ".txt" }) << "\n";

yields "filename". This is useful for example to remove a set of known extensions for a file type, for clean user output. Not all extensions have to be present; those that are not, are simply skipped.

Definition at line 798 of file fs.cpp.

file_exists()

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).

Internally, this function simply returns the value of file_is_readable(), meaning that we also check that the file can actually be read. That is semantically a bit different from just stating that it is a file... But file system stuff in C++ pre-17 is hard, and this works for now.

Definition at line 95 of file fs.cpp.

file_extension()

std::string file_extension

(

std::string const &

filename

)

Return the extension name of a file.

Also see file_filename().

Definition at line 821 of file fs.cpp.

file_filename()

std::string file_filename

(

std::string const &

filename

)

Remove extension if present.

Caveat: Does not remove the path. So, if the filename itself does not contain an extension separator ".", but the path does, this will yield an unwanted result. Call file_basename() first.

Definition at line 811 of file fs.cpp.

file_info()

std::unordered_map< std::string, std::string > file_info

(

std::string const &

filename

)

Return information about a file.

Definition at line 749 of file fs.cpp.

file_is_readable() [1/2]

bool file_is_readable

(

std::string const &

filename

)

Return whether a file is readable.

For this, the file has to exist, and be accessible. Another potential error is that too many files are opened already.

See file_is_readable( std::string const&, std::string& ) for a version of the function that also allows to retrieve the error message in cases where the result is false.

Definition at line 108 of file fs.cpp.

file_is_readable() [2/2]

bool file_is_readable	(	std::string const &	filename,
		std::string &	err_str
	)

Return whether a file is readable, and potentially store the error message.

For this, the file has to exist, and be accessible. Another potential error is that too many files are opened already.

Definition at line 114 of file fs.cpp.

file_output_stream()

void genesis::utils::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  )

inline

Helper function to obtain an output stream to a file.

This function is used internally by all file writers. It makes sure that the file is writable, and throws an exception otherwise.

Furthermore, the function checks whether the path already exists. If it exists and Options::allow_file_overwriting() is not explicitly activated, the function throws, too. This is a safty measure to ensure that users cannot accidentally overwrite their files.

Parameters

[in]	file_name	Path to the file to write to.
[out]	out_stream	Reference to the target output stream. Unfortunately, we cannot return streams, as they do not offer copy or move, so we have to do it this way.
[in]	mode	Mode flag as used by std::ostream.
[in]	create_dirs	Create parent directories if needed.

See also

Options::allow_file_overwriting( bool )

Definition at line 72 of file output_stream.hpp.

file_path()

std::string file_path

(

std::string const &

filename

)

Return the path leading to a file.

Does not resolve the path. Simply splits at the last directory separator. If there is no directory separator, it returns an empty string.

Definition at line 776 of file fs.cpp.

file_read()

std::string file_read	(	std::string const &	filename,
		bool	detect_compression = true
	)

Return the contents of a file as a string.

If the parameter detect_compression is true (default), it is first determined whether the file is gzip compressed, and if so, the file is decompressed when reading.

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

Definition at line 126 of file fs.cpp.

file_read_lines()

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.

If the parameter detect_compression is true (default), it is first determined whether the file is gzip compressed, and if so, the file is decompressed when reading.

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

Definition at line 171 of file fs.cpp.

file_size()

size_t file_size

(

std::string const &

filename

)

Return the size of a file.

Definition at line 762 of file fs.cpp.

file_write()

void file_write	(	std::string const &	content,
		std::string const &	filename,
		bool	create_dirs = true
	)

Write the content of a string to a file.

If the file cannot be written to, the function throws an exception. Also, by default, if the file already exists, an exception is thrown. See Options::allow_file_overwriting() to change this behaviour.

Definition at line 183 of file fs.cpp.

filter_constant_columns()

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.

The Matrix is modified so that all columns c with max(c) - min(c) <= epsilon are removed.

The function returns a sorted list of all column indices of the original matrix that are kept, i.e., that have a greater min-max difference than epsilon. This is useful for e.g., visualising the result of an Edge PCA.

Parameters

[in,out]	data	Matrix to filter inplace.
[in]	epsilon	Maximum deviation for what is considered constant.

Returns

List of original column indices that are kept (not filtered).

Definition at line 158 of file math/matrix.cpp.

finite_maximum()

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

Return the maximum of a range of double values.

Only finite values are used in the comparison. If there are no finite values at all in the range, a quite NaN is returned.

Definition at line 207 of file statistics.hpp.

finite_minimum()

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

Return the minimum of a range of double values.

Only finite values are used in the comparison. If there are no finite values at all in the range, a quite NaN is returned.

Definition at line 175 of file statistics.hpp.

finite_minimum_maximum()

MinMaxPair<double> genesis::utils::finite_minimum_maximum	(	ForwardIterator	first,
		ForwardIterator	last
	)

Return the minimum and the maximum of a range of double values.

Only finite values are used in the comparison. If there are no finite values at all in the range, a quite NaN is returned.

Definition at line 239 of file statistics.hpp.

finite_pairs()

std::pair<std::vector<double>, std::vector<double> > genesis::utils::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.

This function is used for cleaning data input. It iterates both same-length ranges in parallel and copies pairs elements to the two result vectors (one for each range), if both values are finite. The result vectors thus have equal size.

Definition at line 252 of file common.hpp.

fisher_transformation() [1/2]

double genesis::utils::fisher_transformation ( double  correlation_coefficient )

inline

Apply Fisher z-transformation to a correlation coefficient.

The coefficient can be calculated with pearson_correlation_coefficient() or spearmans_rank_correlation_coefficient() and has to be in range [ -1.0, 1.0 ].

There is also a version of this function for a vector of coefficients.

Definition at line 265 of file correlation.hpp.

fisher_transformation() [2/2]

std::vector<double> genesis::utils::fisher_transformation ( std::vector< double > const &  correlation_coefficients )

inline

Apply Fisher z-transformation to a vector of correlation coefficients.

See fisher_transformation( double ) for details.

Definition at line 285 of file correlation.hpp.

for_each_finite_pair()

void genesis::utils::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.

The ranges need to have the same length.

Definition at line 286 of file common.hpp.

fraction_of_variance_unexplained()

double genesis::utils::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.

See https://en.wikipedia.org/wiki/Fraction_of_variance_unexplained for some details.

See also

simple_linear_regression() for calculating such a fit.

Definition at line 155 of file slr.hpp.

from_file()

std::shared_ptr<BaseInputSource> genesis::utils::from_file ( std::string const &  file_name, bool  detect_compression = true  )

inline

Obtain an input source for reading from a file.

The input source returned from this function can be used in the reader classes, e.g., placement::JplaceReader or sequence::FastaReader.

If the parameter detect_compression is true (default), it is first determined whether the file is gzip compressed, and if so, a transparent decompression layer is added. That means, gzip-compressed files can be decompressed automatically and on the fly.

See also

from_files(), from_string(), from_strings(), and from_stream() for similar helper functions for other types of input sources.

Definition at line 68 of file input_source.hpp.

from_files() [1/2]

std::vector<std::shared_ptr<BaseInputSource> > genesis::utils::from_files ( InputIterator  first, InputIterator  last, bool  detect_compression = true  )

inline

Obtain a set of input sources for reading from files.

See from_file() for details. This version returnes multiple input sources from an interator over file names, which can be used for parallely reading from multiple files for speedup.

See also

from_file(), from_string(), from_strings(), and from_stream() for similar helper functions for other types of input sources.

Definition at line 112 of file input_source.hpp.

from_files() [2/2]

std::vector<std::shared_ptr<BaseInputSource> > genesis::utils::from_files ( std::vector< std::string > const &  file_names, bool  detect_compression = true  )

inline

Obtain a set of input sources for reading from files.

See from_file() for details. This version returnes multiple input sources, which can be used for parallely reading from multiple files for speedup. This function can for example be used with the output of utils::dir_list_files().

See also

from_file(), from_string(), from_strings(), and from_stream() for similar helper functions for other types of input sources.

Definition at line 91 of file input_source.hpp.

from_nucleic_acids()

TwobitVector from_nucleic_acids

(

std::string const &

sequence

)

Turn a string of nucleic acids into a TwobitVector.

Definition at line 93 of file utils/math/twobit_vector/functions.cpp.

from_stdin()

std::shared_ptr<BaseInputSource> genesis::utils::from_stdin ( )

inline

Obtain an input source for reading from standard input (i.e., stdin or cin).

The input source returned from this function can be used in the reader classes, e.g., placement::JplaceReader or sequence::FastaReader.

See also

from_file(), from_files(), from_string(), and from_strings() for similar helper functions for other types of input sources, and see from_stream() for the underlying stream input helper function.

Definition at line 205 of file input_source.hpp.

from_stream()

std::shared_ptr<BaseInputSource> genesis::utils::from_stream ( std::istream &  input_stream )

inline

Obtain an input source for reading from a stream.

The input source returned from this function can be used in the reader classes, e.g., placement::JplaceReader or sequence::FastaReader.

See also

from_file(), from_files(), from_string(), and from_strings() for similar helper functions for other types of input sources.

Definition at line 189 of file input_source.hpp.

from_string()

std::shared_ptr<BaseInputSource> genesis::utils::from_string ( std::string const &  input_string )

inline

Obtain an input source for reading from a string.

The input source returned from this function can be used in the reader classes, e.g., placement::JplaceReader or sequence::FastaReader.

See also

from_file(), from_files(), from_strings(), and from_stream() for similar helper functions for other types of input sources.

Definition at line 134 of file input_source.hpp.

from_strings() [1/2]

std::vector<std::shared_ptr<BaseInputSource> > genesis::utils::from_strings ( InputIterator  first, InputIterator  last  )

inline

Obtain a set of input sources for reading from strings.

See from_string() and from_files() for details.

See also

from_file(), from_files(), from_string(), and from_stream() for similar helper functions for other types of input sources.

Definition at line 167 of file input_source.hpp.

from_strings() [2/2]

std::vector<std::shared_ptr<BaseInputSource> > genesis::utils::from_strings ( std::vector< std::string > const &  input_strings )

inline

Obtain a set of input sources for reading from strings.

See from_string() and from_files() for details.

See also

from_file(), from_files(), from_string(), and from_stream() for similar helper functions for other types of input sources.

Definition at line 148 of file input_source.hpp.

geo_distance()

double geo_distance	(	GeoCoordinate const &	c1,
		GeoCoordinate const &	c2
	)

Calculate the distance (in km) between two points on Earth.

Uses the Haversine formula. See convert_geo_coordinate() for a conversion function for geographical coordinates.

Definition at line 317 of file utils/tools/geodesy/functions.cpp.

geometric_mean() [1/2]

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

Calculate the geometric mean 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. The function then calculates the geometric mean of all positive 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. If finite non-positive numbers (zero or negative) are found, an exception is thrown.

See also

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

weighted_geometric_mean() for a weighted version.

arithmetic_mean() for a function that calculates the arithmetic mean, and

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

Definition at line 574 of file statistics.hpp.

geometric_mean() [2/2]

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

inline

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

See also

geometric_mean( ForwardIterator first, ForwardIterator last ) for details.

arithmetic_mean() for a function that calculates the arithmetic mean, and

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

Definition at line 613 of file statistics.hpp.

get_attribute_string_()

static std::string genesis::utils::get_attribute_string_ ( Style const &  s )

static

Internal helper function that returns the attribute string of a Style based on its properties.

Definition at line 193 of file style.cpp.

get_background_color_iterator()

static std::array<std::pair<std::string, std::string>, 17>::const_iterator genesis::utils::get_background_color_iterator ( std::string  name )

static

Internal helper function that returns an iterator into the background color list.

Definition at line 69 of file style.cpp.

get_color_list_iterator_()

static NamedColorList::const_iterator genesis::utils::get_color_list_iterator_ ( NamedColorList const &  list, std::string  name  )

static

Internal helper function.

Returns an iterator into the vector if the given name is a named color or an iterator to the end of the color map if it is not a named color.

Definition at line 1465 of file names.cpp.

get_core_id_()

size_t genesis::utils::get_core_id_

(

std::string const &

cpu_path

)

Definition at line 986 of file info.cpp.

get_cpu_model_()

std::string genesis::utils::get_cpu_model_

(

)

Definition at line 578 of file info.cpp.

get_cpuid_()

void genesis::utils::get_cpuid_	(	int32_t	out[4],
		int32_t	eax,
		int32_t	ecx
	)

Definition at line 468 of file info.cpp.

get_foreground_color_iterator()

static std::array<std::pair<std::string, std::string>, 17>::const_iterator genesis::utils::get_foreground_color_iterator ( std::string  name )

static

Internal helper function that returns an iterator into the foreground color list.

Definition at line 51 of file style.cpp.

get_memtotal_()

size_t genesis::utils::get_memtotal_

(

)

Definition at line 609 of file info.cpp.

get_numa_node_id_()

size_t genesis::utils::get_numa_node_id_

(

std::string const &

cpu_path

)

Definition at line 971 of file info.cpp.

get_physical_core_count_()

int genesis::utils::get_physical_core_count_

(

size_t

n_cpu

)

Definition at line 991 of file info.cpp.

get_vendor_string_()

std::string genesis::utils::get_vendor_string_

(

)

Definition at line 564 of file info.cpp.

glm_coefficients() [1/2]

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().

Overload where the link function can be specified, for links other than identity.

Note that the functions glm_estimate_intercept() and glm_estimate_betas() compute their values in the original space of the predictors and response, and not on the link scale. This is particularly important when using a link function other than identity. See glm_estimate_intercept() for an example of the value computed.

Definition at line 783 of file glm.cpp.

glm_coefficients() [2/2]

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().

This simply calls glm_estimate_intercept() and glm_estimate_betas(), and stores the results in a vector, i.e., the intercept, followed by the beta coefficients. This is hence a convenience function for cases where all coefficients are needed. See these two functions for specifics on the values that they are computing.

Assumes identity link function such as from glm_link_identity(). See the other overload of the function to specify the link function.

Definition at line 775 of file glm.cpp.

glm_convert_dataframe() [1/2]

Matrix< double > glm_convert_dataframe

(

Dataframe const &

df

)

Definition at line 223 of file dataframe.cpp.

glm_convert_dataframe() [2/2]

Matrix< double > glm_convert_dataframe	(	Dataframe const &	df,
		std::vector< std::string >	row_order
	)

Definition at line 187 of file dataframe.cpp.

glm_estimate_betas()

std::vector< double > glm_estimate_betas

(

GlmOutput const &

output

)

Compute the beta estimates resulting from a glm_fit().

The GlmOutput::betaQ result expresses the betas in terms of the GlmOutput::Xb basis space, which is an orthogonal representaton of the original predictor matrix. To turn this into betas expressed in the original predictor column space, this function inverts the triangular transformation matrix GlmOutput::tri, and uses this to transform the betaQ into betas.

Definition at line 605 of file glm.cpp.

glm_estimate_betas_and_var_covar()

std::pair<std::vector<double>, std::vector<double> > genesis::utils::glm_estimate_betas_and_var_covar	(	GlmOutput const &	output,
		std::vector< double > const &	meat
	)

Definition at line 693 of file glm.cpp.

glm_estimate_betas_inv_tri_()

std::vector<double> genesis::utils::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.

Definition at line 582 of file glm.cpp.

glm_estimate_intercept() [1/2]

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().

Overload where the link function can be specified, for links other than identity.

Note that this function computes the intercept in the original space of the predictors and response. For instance, assuming the data has been generated like this:

beta_0 = 0.5
beta_1 = 0.3
X = np.linspace(start=1, stop=10, num=10)
Y = np.exp(beta_0 + beta_1 * X)

and the GLM has accordingly been run with glm_family_poisson()/glm_link_log(), that is, with a log link. Then, this function here computes the intercept as originally specified, i.e., 0.5.

Definition at line 725 of file glm.cpp.

glm_estimate_intercept() [2/2]

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().

This takes the input and output of the glm_fit(), as well as the list of betas in the original predictor column space, which is computed by glm_estimate_betas().

Assumes identity link function such as from glm_link_identity(). See the other overload of the function to specify the link function.

Definition at line 714 of file glm.cpp.

glm_factor() [1/3]

GlmFactor<typename ForwardIterator::value_type> genesis::utils::glm_factor	(	ForwardIterator	first,
		ForwardIterator	last
	)

Definition at line 166 of file factor.hpp.

glm_factor() [2/3]

GlmFactor<typename ForwardIterator::value_type> genesis::utils::glm_factor	(	ForwardIterator	first,
		ForwardIterator	last,
		std::vector< typename ForwardIterator::value_type > const &	levels
	)

Definition at line 152 of file factor.hpp.

glm_factor() [3/3]

GlmFactor<typename ForwardIterator::value_type> genesis::utils::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.

The function takes a range (first to last, with last being the past-the-end element) and finds all unique values (called levels) in the range. These are stored in the GlmFactor::levels set of the result. The provided values in the given range are then encoded in GlmFactor::values using the indices of the unique values in the levels.

If the parameter levels is not provided, the found unique levels are sorted. If however levels are provided, these are used instead, and their ordering is used for the encoding of the values. Any value that is not found in the provided levels is assigned max size_t as an indicator of an unused/missing level.

The paramter exclude works similary: All levels in the exlcude list are removed from the result (no matter whether levels were provided or the found ones are used), and all corresponding values are encoded as max size_t.

Definition at line 88 of file factor.hpp.

glm_factor_summary()

std::vector<size_t> genesis::utils::glm_factor_summary

(

GlmFactor< T > const &

factor

)

Get the number of occurrences of each level in a GlmFactor.

The resulting vector indicates how often each level of the factor occurs in its values, using the same indices as the levels:

// List the number of occurrences for each factor.
auto const smry = glm_factor_summary( factor );
for( size_t i = 0; i < factor.levels.size(); ++i ) {
 std::cout << "Level " << factor.levels[i] << ": " << smry[i];
}

This is for example useful for user output.

Definition at line 193 of file factor.hpp.

glm_family_binomial()

GlmFamily genesis::utils::glm_family_binomial ( )

inline

Binomial family functions.

The canonical link for binomial is logit, see glm_link_logit().

Definition at line 120 of file family.hpp.

glm_family_gamma()

GlmFamily genesis::utils::glm_family_gamma ( )

inline

Gamma family functions.

The canonical link for gamma is identity, see glm_link_gamma().

Definition at line 266 of file family.hpp.

glm_family_gaussian()

GlmFamily genesis::utils::glm_family_gaussian ( )

inline

Gaussian/normal family functions.

The canonical link for gaussian/normal is identity, see glm_link_identity().

Definition at line 226 of file family.hpp.

glm_family_poisson()

GlmFamily genesis::utils::glm_family_poisson ( )

inline

Poisson family functions.

The canonical link for poisson is log, see glm_link_log().

Definition at line 181 of file family.hpp.

glm_fit() [1/3]

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.

See the Acknowledgements for details on the license and original authors.

Definition at line 532 of file glm.cpp.

glm_fit() [2/3]

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).

Uses the canonical link function of the provided distribution family.

See the Acknowledgements for details on the license and original authors.

Definition at line 519 of file glm.cpp.

glm_fit() [3/3]

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).

See the Acknowledgements for details on the license and original authors.

Definition at line 355 of file glm.cpp.

glm_gaussian_()

static void genesis::utils::glm_gaussian_ ( Matrix< double > const &  x_predictors, std::vector< double > const &  y_response, GlmExtras const &  extras, GlmControl const &  control, GlmFreedom const &  freedom, GlmOutput &  result  )

static

Definition at line 264 of file glm.cpp.

glm_indicator_variables() [1/2]

Dataframe genesis::utils::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.

The function uses the most common level as reference level, and otherwise behaves the same as glm_indicator_variables().

Definition at line 302 of file factor.hpp.

glm_indicator_variables() [2/2]

Dataframe genesis::utils::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.

The function takes a factor object, and for its k levels creates k - 1 dummy indicator variables that encode the factors for regression. The given reference_level is excluded, and for all other levels, a column is returned that contains 1.0 wherever the values of the factor are equal to that level, and 0.0 otherwise. Missing/exluded levels are encoded as NaN.

Definition at line 214 of file factor.hpp.

glm_inv_tri_()

std::vector<double> genesis::utils::glm_inv_tri_	(	std::vector< double > const &	tri,
		size_t	M
	)

Invert diagonal and unit upper triangular matrices stored as one array.

Definition at line 549 of file glm.cpp.

glm_irls_()

static void genesis::utils::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  )

static

Definition at line 81 of file glm.cpp.

glm_link_identity()

GlmLink genesis::utils::glm_link_identity ( )

inline

Identity link functions.

The canonical family for identiy is normal/gaussian, see glm_family_gaussian().

Definition at line 153 of file utils/math/regression/link.hpp.

glm_link_inverse()

GlmLink genesis::utils::glm_link_inverse ( )

inline

Inverse link functions.

The canonical family for inverse is gamma, see glm_family_gamma().

Definition at line 182 of file utils/math/regression/link.hpp.

glm_link_log()

GlmLink genesis::utils::glm_link_log ( )

inline

Log link functions.

The canonical family for logit is poisson, see glm_family_poisson().

Definition at line 125 of file utils/math/regression/link.hpp.

glm_link_logit()

GlmLink genesis::utils::glm_link_logit ( )

inline

Logit link functions.

The canonical family for logit is binomial, see glm_family_binomial().

Definition at line 97 of file utils/math/regression/link.hpp.

glm_prepare_dataframe() [1/2]

Dataframe glm_prepare_dataframe

(

Dataframe const &

df

)

Definition at line 181 of file dataframe.cpp.

glm_prepare_dataframe() [2/2]

Dataframe glm_prepare_dataframe	(	Dataframe const &	df,
		std::string &	report
	)

Definition at line 51 of file dataframe.cpp.

gradient()

Color gradient	(	std::map< double, Color > const &	ranges,
		double	value
	)

Returns a Color that is created using a color gradient.

The function takes a color gradient in form of a map from double to Color. The keys in the map are offset positions (stops) with specific Colors assigned to them. An arbitrary number of keys in between these boundaries is allowed.

Each key is associated with a Color value, which indicates the color at that position.

Example:

// Prepare gradient ranges.
auto ranges = std::map<double, Color>();
ranges[ 0.0 ] = Color( 0.0, 1.0, 0.0 );
ranges[ 0.5 ] = Color( 1.0, 1.0, 0.0 );
ranges[ 1.0 ] = Color( 1.0, 0.0, 0.0 );

// Get color at 30% of the green-yellow-red gradient.
Color c = gradient( ranges, 0.3 );

This map defines the same gradient that is used for heat_gradient. The range boundaries do not have to be [ 0.0, 1.0 ]. They can be set to any range that is needed to reflect the range of possible values.

The second parameter of this function then takes the position at which the gradient is evaluated. Values outside of the interval that is defined by the range are set to the closest interval border value.

For example, given the range map above, a value of 0.0 gives green; 0.5 gives yellow; 1.0 gives red; values in between are interpolated linearily.

Definition at line 170 of file utils/color/functions.cpp.

guess_number_of_threads()

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.

This function uses multiple sources and ways to try to guess a reasonable number of threads:

• If use_openmp is set, we use the omp_get_max_threads() function or the OMP_NUM_THREADS environment variable to get a number of threads, using the info_number_of_threads_openmp() function. For details, see there.
• If use_slurm is set, we get a number of cores from the environment variable SLURM_CPUS_PER_TASK.
• Lastly, we get the result of std::thread::hardware_concurrency() as another hint. If furthermore physical_cores is set, and hyperthreads are enabled, we divide that hardware concurrency number by two, in order to account for hyperthreads, resulting in the number of physical cores available on the system (ideally). This avoids core oversubscription that could otherwise be the result of using all threads instead of all physical cores.

If the numbers disagree with each other, we prefer OpenMP over slurm over hardware_concurrency(), that is, we are going from most specific to least. Furthermore, if the OpenMP based guess yields exactly the same number as the hardware concurrency, we also use the physical_cores setting, as this result usually indicates that OpenMP left at its default, in which case we also want to avoid core oversubscription due to hyperthreading.

The function is guaranteed to return a non-zero value, meaning that at least the main thread is always accounted for. This is important for Options::get().init_global_thread_pool(), which will account for that, and initialize the number of additional threads to one fewer than this.

Definition at line 1078 of file info.cpp.

harmonic_mean() [1/2]

double genesis::utils::harmonic_mean	(	ForwardIterator	first,
		ForwardIterator	last,
		HarmonicMeanZeroPolicy	zero_policy = HarmonicMeanZeroPolicy::kThrow
	)

Calculate the harmonic mean 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. The function then calculates the harmonic mean of all non-negative or positive (depending on the zero_policy) 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. If finite negative numbers are found, an exception is thrown. Zero values are treated according to the zero_policy.

See also

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

weighted_harmonic_mean() for a weighted version.

arithmetic_mean() for a function that calculates the arithmetic mean, and

geometric_mean() for a function that calculates the geometric mean.

Definition at line 775 of file statistics.hpp.

harmonic_mean() [2/2]

double genesis::utils::harmonic_mean ( std::vector< double > const &  vec, HarmonicMeanZeroPolicy  zero_policy = HarmonicMeanZeroPolicy::kThrow  )

inline

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

See also

harmonic_mean( ForwardIterator first, ForwardIterator last ) for details.

arithmetic_mean() for a function that calculates the arithmetic mean, and

geometric_mean() for a function that calculates the geometric mean.

Definition at line 849 of file statistics.hpp.

hash_combine()

constexpr std::size_t genesis::utils::hash_combine ( std::size_t  seed, T const &  value  )

inlineconstexpr

Combine a seed value (e.g., another hash) with the hash of a given type.

Definition at line 160 of file std.hpp.

hash_hex()

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.

See HashingFunctions for the list of available hashing functions.

Definition at line 47 of file utils/tools/hash/functions.cpp.

head()

std::string head	(	std::string const &	text,
		size_t	lines
	)

Return the first lines of the text.

Definition at line 496 of file string.cpp.

heat_gradient()

Color heat_gradient

(

double

percentage

)

Return a Color that represents a heat gradient for a given percentage value.

Given a percentage value in the range of [ 0.0, 1.0], the functions represents the heat of that value. For 0.0, the heat gradient value is green, for 0.5 yellow and for 1.0 red. The values in between are interpolated linearily.

Definition at line 203 of file utils/color/functions.cpp.

heat_map_matrix_range_()

Matrix<utils::Color> genesis::utils::heat_map_matrix_range_	(	Matrix< double > const &	values,
		HeatmapParameters const &	parameters
	)

Definition at line 136 of file heat_map.cpp.

heat_map_matrix_range_all_()

Matrix<utils::Color> genesis::utils::heat_map_matrix_range_all_	(	Matrix< double > const &	values,
		HeatmapParameters const &	parameters
	)

Definition at line 67 of file heat_map.cpp.

heat_map_matrix_range_col_()

Matrix<utils::Color> genesis::utils::heat_map_matrix_range_col_	(	Matrix< double > const &	values,
		HeatmapParameters const &	parameters
	)

Definition at line 111 of file heat_map.cpp.

heat_map_matrix_range_row_()

Matrix<utils::Color> genesis::utils::heat_map_matrix_range_row_	(	Matrix< double > const &	values,
		HeatmapParameters const &	parameters
	)

Definition at line 89 of file heat_map.cpp.

heat_map_matrix_update_min_max_()

MinMaxPair<double> genesis::utils::heat_map_matrix_update_min_max_	(	MinMaxPair< double > const &	min_max,
		HeatmapParameters const &	parameters
	)

Definition at line 52 of file heat_map.cpp.

hypergeometric_distribution()

size_t hypergeometric_distribution	(	size_t	n1,
		size_t	n2,
		size_t	t
	)

Select a random sample from a hypergeometric distribution.

This is the distribution of drawing balls without replacement from an urn with two colors. Here, n1 and n2 are the numbers of balls of each color, and t is the number of balls to sample, and the return value is the number of balls of the first color. See https://en.wikipedia.org/wiki/Hypergeometric_distribution

Definition at line 401 of file distribution.cpp.

hypergeometric_distribution_gsl()

size_t genesis::utils::hypergeometric_distribution_gsl	(	size_t	n1,
		size_t	n2,
		size_t	t
	)

Definition at line 463 of file distribution.cpp.

hypergeometric_distribution_inversion_mode_()

size_t genesis::utils::hypergeometric_distribution_inversion_mode_	(	size_t	n,
		size_t	m,
		size_t	N
	)

Definition at line 279 of file distribution.cpp.

hypergeometric_distribution_ratio_of_unifoms_()

size_t genesis::utils::hypergeometric_distribution_ratio_of_unifoms_	(	size_t	n,
		size_t	m,
		size_t	N
	)

Definition at line 176 of file distribution.cpp.

indent()

std::string indent	(	std::string const &	text,
		std::string const &	indentation = "    "
	)

Indent each line of text with indentation and return the result.

By default, four spaces are used to indent. Whether the text ends with a new line or not is not changed. Any trailing indentation chars are trimmed, in order to not have trailing whitespaces in the result (except for the new line, if the text ends in one).

Definition at line 719 of file string.cpp.

index_of_dispersion() [1/2]

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

inline

Calculate the index of dispersion.

The index of dispersion, also known as the dispersion index, coefficient of dispersion, relative variance, variance-to-mean ratio (VMR) or Fano factor, is defined as the ratio of the variance to the mean. Variance is the square of the standard deviation. See mean_stddev() to calculate those values. See https://en.wikipedia.org/wiki/Index_of_dispersion for details.

Definition at line 1151 of file statistics.hpp.

index_of_dispersion() [2/2]

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

inline

Calculate the index of dispersion.

The index of dispersion, also known as the dispersion index, coefficient of dispersion, relative variance, variance-to-mean ratio (VMR) or Fano factor, is defined as the ratio of the variance to the mean. Variance is the square of the standard deviation. See mean_stddev() to calculate those values. See https://en.wikipedia.org/wiki/Index_of_dispersion for details.

Definition at line 1159 of file statistics.hpp.

info_get_compiler()

InfoCompiler const & info_get_compiler

(

)

Return information about compiler settings and flags.

Definition at line 171 of file info.cpp.

info_get_hardware()

InfoHardware const & info_get_hardware

(

)

Return information about hardware features.

Definition at line 665 of file info.cpp.

info_get_pid()

size_t info_get_pid

(

)

Get the process ID of the current process.

This is a POSIX system call, using getpid(). See https://man7.org/linux/man-pages/man2/getpid.2.html and https://developer.apple.com/library/archive/documentation/System/Conceptual/ManPages_iPhoneOS/man2/getpid.2.html for details. We wrap this here to avoid having the system headers included. Furthermore, we convert to a size_t for convenience, although typically, the pid is an int (guaranteed to be non-negative for an actual process).

Definition at line 1133 of file info.cpp.

info_hyperthreads_enabled()

bool info_hyperthreads_enabled

(

)

Try to get whether hyperthreads are enabled in the current system.

Definition at line 1028 of file info.cpp.

info_number_of_threads_openmp()

size_t info_number_of_threads_openmp

(

)

Get the number of threads as indicated by the OpenMP environment.

If genesis was compiled with OpenMP support (that is, if GENESIS_OPENMP is defined, which is done via the CMake script), we use omp_get_max_threads() to get a number of threads from that. If however genesis was compiled without OpenMP support, we instead consider the environment variable OMP_NUM_THREADS as a source for the OpenMP threads.

If unsuccessful, 0 is returned.

Definition at line 1044 of file info.cpp.

info_number_of_threads_slurm()

size_t info_number_of_threads_slurm

(

)

Get the number of threads as indicated by the SLURM environment.

This uses the environment variable SLURM_CPUS_PER_TASK. If unsuccessful, 0 is returned.

Definition at line 1067 of file info.cpp.

info_online_cpu_cores()

long genesis::utils::info_online_cpu_cores

(

)

Definition at line 954 of file info.cpp.

info_physical_core_count()

size_t info_physical_core_count

(

)

Get the number of CPU cores.

This tries to get the physical core count, and if that fails, it uses std::thread::hardware_concurrency() along with info_hyperthreads_enabled() to determine a best guess at the number of physical cores.

Definition at line 1010 of file info.cpp.

info_preprocessor_definitions()

std::unordered_map< std::string, std::string > const & info_preprocessor_definitions

(

)

Return a string map with some relevant preprocessor macros.

This is mostly for debugging, to see how different systems compile the code. We only add a set of important macros that we internally have use for as well.

Definition at line 296 of file info.cpp.

info_print_compiler()

std::string info_print_compiler

(

)

Print information about compiler settings and flags to a string.

Definition at line 363 of file info.cpp.

info_print_hardware()

std::string info_print_hardware

(

bool

full = false

)

Print information about hardware features to a string.

This lists hardware features such as memory, CPU model, and potentially CPU features. If full is given, each CPU feature that we test for is listed. Otherwise, by default, we just print a summary of the features that are important to us, such as AVX.

Definition at line 795 of file info.cpp.

info_process_current_cpu_usage()

double info_process_current_cpu_usage	(	bool	all_cores = true,
		bool	percent = true
	)

Return the CPU usage of the current process.

The first time the function is called, it is being initialized, and will return 0.0, as there is no usage to be reported yet. Any subsequent call with then report the usage since the last call.

By default, this reports the total usage across all cores. That is, for multi-core systems, this can report usage up to the number of cores. For instance, two cores fully running on a 4-core system would report 200% usage (using return value 200.0 by default, or 2.0 if percent is set to false). If however all_cores is set to false, this is instead divided by the number of cores, and so would return 50% usage (using return value 50.0 or 0.5, depending on percent) instead.

Definition at line 1891 of file info.cpp.

info_process_current_file_count()

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.

Definition at line 1213 of file info.cpp.

info_process_current_memory_usage()

size_t info_process_current_memory_usage

(

)

Return the memory currently used by the current process, in bytes.

Definition at line 1876 of file info.cpp.

info_process_max_file_count()

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.

Definition at line 1200 of file info.cpp.

info_process_peak_memory_usage()

size_t info_process_peak_memory_usage

(

)

Get the peak used memory, in bytes.

Definition at line 1911 of file info.cpp.

info_process_print_total_usage()

std::string info_process_print_total_usage

(

)

Print usage information to a string.

Definition at line 1971 of file info.cpp.

info_process_total_cpu_time()

std::pair< double, double > info_process_total_cpu_time

(

)

Get the currently used cpu run time, similar to the Unix time command.

Time is returned in seconds, with the first result the user time, and the second the system time.

Definition at line 1927 of file info.cpp.

info_process_total_energy_consumption()

double info_process_total_energy_consumption

(

)

Get energy consumption of the program so far, in Wh.

Definition at line 1940 of file info.cpp.

info_stderr_is_terminal()

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.

Definition at line 1163 of file info.cpp.

info_stdin_is_terminal()

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.

Definition at line 1144 of file info.cpp.

info_stdout_is_terminal()

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.

Definition at line 1154 of file info.cpp.

info_system_current_cpu_usage()

double info_system_current_cpu_usage	(	bool	all_cores = true,
		bool	percent = true
	)

Return the CPU usage of the system, across all cores.

See also

See info_process_current_cpu_usage() for details on the parameters.

Definition at line 1898 of file info.cpp.

info_system_current_memory_available()

size_t info_system_current_memory_available

(

)

Return the memory currently available in the system, in bytes.

Definition at line 1886 of file info.cpp.

info_system_current_memory_usage()

size_t info_system_current_memory_usage

(

)

Return the memory currently used across all running processes, in bytes.

Definition at line 1881 of file info.cpp.

info_task_cpu_cores()

unsigned int genesis::utils::info_task_cpu_cores

(

bool

physical = false

)

Definition at line 934 of file info.cpp.

info_terminal_size()

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.

Definition at line 1172 of file info.cpp.

info_use_avx()

bool info_use_avx

(

)

Assess if it is safe to use AVX features.

This is the case if the hardware supports AVX, the OS has it activated, and the compiler had the respective flag set.

Definition at line 897 of file info.cpp.

info_use_avx2()

bool info_use_avx2

(

)

Assess if it is safe to use AVX2 features.

This is the case if the hardware supports AVX2, the OS has it activated, and the compiler had the respective flag set.

Definition at line 908 of file info.cpp.

info_use_avx512()

bool info_use_avx512

(

)

Assess if it is safe to use AVX512 features.

This is the case if the hardware supports AVX512, the OS has it activated, and the compiler had the respective flag set.

Definition at line 919 of file info.cpp.

insert_sorted() [1/2]

std::vector<T>::iterator genesis::utils::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.

Definition at line 152 of file algorithm.hpp.

insert_sorted() [2/2]

std::vector<T>::iterator genesis::utils::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.

Definition at line 166 of file algorithm.hpp.

int_pow()

size_t genesis::utils::int_pow ( size_t  base, size_t  exp  )

inline

Calculate the power base^exp for positive integer values.

Remark: This overflows quite easily. The function does not check whether the desired power actually fits within size_t. Use is_valid_int_pow() to check for this first.

Rationale for this function: One could argue that int powers are not really useful, particularly because of the fast overflow. However, using doubles leads to rounding errors, at least for bigger numbers. So, within the valid range, this function is more accurate. Also, it is faster.

Definition at line 191 of file common.hpp.

interpolate()

Color interpolate	(	Color const &	color1,
		Color const &	color2,
		double	fraction
	)

Linearily interpolate between two Colors.

Definition at line 154 of file utils/color/functions.cpp.

is_alnum()

constexpr bool genesis::utils::is_alnum ( char  c )

constexprnoexcept

Return whether a char is a letter (a-z or A-Z) or a digit (0-9), ASCII-only.

Definition at line 143 of file char.hpp.

is_alpha()

constexpr bool genesis::utils::is_alpha ( char  c )

constexprnoexcept

Return whether a char is a letter (a-z or A-Z), ASCII-only.

Definition at line 135 of file char.hpp.

is_ascii() [1/3]

constexpr bool genesis::utils::is_ascii ( char  c )

constexprnoexcept

Return whether a char is pure ASCII, that is, in the range [0, 127].

Definition at line 69 of file char.hpp.

is_ascii() [2/3]

constexpr bool genesis::utils::is_ascii ( std::false_type  , T  c  )

constexprnoexcept

Implementation detail for is_ascii(char).

Definition at line 60 of file char.hpp.

is_ascii() [3/3]

constexpr bool genesis::utils::is_ascii ( std::true_type  , T  c  )

constexprnoexcept

Implementation detail for is_ascii(char).

Definition at line 50 of file char.hpp.

is_blank()

constexpr bool genesis::utils::is_blank ( char  c )

constexprnoexcept

Return whether a char is either a space or a tab character.

Definition at line 174 of file char.hpp.

is_canonical_link()

bool genesis::utils::is_canonical_link ( GlmFamily const &  family, GlmLink const &  link  )

inline

Definition at line 106 of file family.hpp.

is_cntrl()

constexpr bool genesis::utils::is_cntrl ( char  c )

constexprnoexcept

Return whether a char is a control character, according to iscntrl of the cctype> heade but ASCII-only.

Definition at line 79 of file char.hpp.

is_color_name()

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().

Definition at line 1504 of file names.cpp.

is_color_name_lego()

bool is_color_name_lego

(

std::string const &

name

)

Return true iff the given name is a named LEGO color.

Names are compared only by their alnum chars, and the letter case is ignored. See color_from_name_lego() for details on this color list.

Definition at line 1587 of file names.cpp.

is_color_name_web()

bool is_color_name_web

(

std::string const &

name

)

Return true iff the given name is a named web color.

Names are compared only by their alnum chars, and the letter case is ignored.

Definition at line 1537 of file names.cpp.

is_color_name_xkcd()

bool is_color_name_xkcd

(

std::string const &

name

)

Return true iff the given name is a named xkcd color.

Names are compared only by their alnum chars, and the letter case is ignored. See color_from_name_xkcd() for details on this color list.

Definition at line 1562 of file names.cpp.

is_control()

constexpr bool genesis::utils::is_control ( char  c )

constexprnoexcept

Return whether a char is a control character, excluding white spaces, ASCII-only.

Definition at line 87 of file char.hpp.

is_convertible_to_bool() [1/4]

bool is_convertible_to_bool	(	Dataframe const &	df,
		size_t	col_index
	)

Definition at line 61 of file utils/containers/dataframe/operators.cpp.

is_convertible_to_bool() [2/4]

bool is_convertible_to_bool	(	Dataframe const &	df,
		std::string const &	col_name
	)

Definition at line 78 of file utils/containers/dataframe/operators.cpp.

is_convertible_to_bool() [3/4]

bool genesis::utils::is_convertible_to_bool	(	ForwardIterator	first,
		ForwardIterator	last
	)

Definition at line 162 of file convert.hpp.

is_convertible_to_bool() [4/4]

bool is_convertible_to_bool

(

std::string const &

str

)

Return whether a string can be converted to bool.

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 74 of file convert.cpp.

is_convertible_to_bool_double() [1/2]

bool genesis::utils::is_convertible_to_bool_double	(	ForwardIterator	first,
		ForwardIterator	last
	)

Definition at line 225 of file convert.hpp.

is_convertible_to_bool_double() [2/2]

bool is_convertible_to_bool_double

(

std::string const &

str

)

Return whether a string can be converted to bool (and stored as a double).

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 112 of file convert.cpp.

is_convertible_to_double() [1/4]

bool is_convertible_to_double	(	Dataframe const &	df,
		size_t	col_index
	)

Definition at line 84 of file utils/containers/dataframe/operators.cpp.

is_convertible_to_double() [2/4]

bool is_convertible_to_double	(	Dataframe const &	df,
		std::string const &	col_name
	)

Definition at line 100 of file utils/containers/dataframe/operators.cpp.

is_convertible_to_double() [3/4]

bool genesis::utils::is_convertible_to_double	(	ForwardIterator	first,
		ForwardIterator	last
	)

Definition at line 278 of file convert.hpp.

is_convertible_to_double() [4/4]

bool is_convertible_to_double

(

std::string const &

str

)

Return whether a string can be converted to double.

Definition at line 172 of file convert.cpp.

is_convertible_to_signed_integer() [1/2]

bool genesis::utils::is_convertible_to_signed_integer	(	ForwardIterator	first,
		ForwardIterator	last
	)

Definition at line 331 of file convert.hpp.

is_convertible_to_signed_integer() [2/2]

bool is_convertible_to_signed_integer

(

std::string const &

str

)

Return whether a string can be converted to signed integer.

Definition at line 204 of file convert.cpp.

is_convertible_to_tm() [1/6]

bool genesis::utils::is_convertible_to_tm	(	ForwardIterator	first,
		ForwardIterator	last
	)

Return whether a list of std::string is convertible to std::tm date/time objects.

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.

Definition at line 405 of file date_time.hpp.

is_convertible_to_tm() [2/6]

bool genesis::utils::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.

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

Definition at line 383 of file date_time.hpp.

is_convertible_to_tm() [3/6]

bool genesis::utils::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.

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

Definition at line 361 of file date_time.hpp.

is_convertible_to_tm() [4/6]

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.

The function tries to guess the format. See convert_to_tm( std::string const& ) for details.

Definition at line 381 of file date_time.cpp.

is_convertible_to_tm() [5/6]

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.

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

Definition at line 368 of file date_time.cpp.

is_convertible_to_tm() [6/6]

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.

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

Definition at line 361 of file date_time.cpp.

is_convertible_to_unsigned_integer() [1/2]

bool genesis::utils::is_convertible_to_unsigned_integer	(	ForwardIterator	first,
		ForwardIterator	last
	)

Definition at line 384 of file convert.hpp.

is_convertible_to_unsigned_integer() [2/2]

bool is_convertible_to_unsigned_integer

(

std::string const &

str

)

Return whether a string can be converted to unsigned integer.

Definition at line 236 of file convert.cpp.

is_defined() [1/2]

bool genesis::utils::is_defined ( GlmFamily const &  family )

inline

Check whether all necessary values and functors of a GlmFamily are set.

Definition at line 101 of file family.hpp.

is_defined() [2/2]

bool genesis::utils::is_defined ( GlmLink const &  link )

inline

Check whether all necessary values and functors of a GlmLink are set.

Definition at line 83 of file utils/math/regression/link.hpp.

is_digit()

constexpr bool genesis::utils::is_digit ( char  c )

constexprnoexcept

Return whether a char is a digit (0-9), ASCII-only.

Definition at line 95 of file char.hpp.

is_dir()

bool is_dir

(

std::string const &

path

)

Return true iff the provided path is a directory.

Internally, this function simply return the value of dir_exists(), as this already does the needed check. Thus, it is an alias.

Definition at line 213 of file fs.cpp.

is_file()

bool is_file

(

std::string const &

path

)

Return true iff the provided path is a (readable) file.

Internally, this function simply returns the value of file_is_readable(), meaning that we also check that the file can actually be read. That is semantically a bit different from just stating that it is a file... But file system stuff in C++ pre-17 is hard, and this works for now.

Definition at line 90 of file fs.cpp.

is_graph()

constexpr bool genesis::utils::is_graph ( char  c )

constexprnoexcept

Return whether a char is a character with graphical representation, according to isgraph of the cctype header, but ASCII-only.

Definition at line 166 of file char.hpp.

is_gzip_compressed_file()

bool is_gzip_compressed_file

(

std::string const &

file_name

)

Return whether a given file is gzip-compressed.

Returns true only iff the file exists and is gzip-compressed. If there is a mismatch between the gzip magic bytes and the file ending, a warning is issued via LOG_WARN.

Definition at line 58 of file gzip.cpp.

is_lower()

constexpr bool genesis::utils::is_lower ( char  c )

constexprnoexcept

Return whether a char is a lower case letter (a-z), ASCII-only.

Definition at line 115 of file char.hpp.

is_newline()

constexpr bool genesis::utils::is_newline ( char  c )

constexprnoexcept

Return whether a char is either a new line or a carriage return character.

Definition at line 182 of file char.hpp.

is_numerical_type_()

static bool genesis::utils::is_numerical_type_ ( Dataframe const &  df, size_t  col_index  )

static

Definition at line 51 of file utils/containers/dataframe/operators.cpp.

is_other_space()

constexpr bool genesis::utils::is_other_space ( char  c )

constexprnoexcept

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.

Definition at line 191 of file char.hpp.

is_print()

constexpr bool genesis::utils::is_print ( char  c )

constexprnoexcept

Return whether a char is a printable character, according to isprint of the cctype header, but ASCII-only.

Definition at line 209 of file char.hpp.

is_punct()

constexpr bool genesis::utils::is_punct ( char  c )

constexprnoexcept

Return whether a char is a punctuation mark, according to ispunct of the cctype header, but ASCII-only.

Definition at line 152 of file char.hpp.

is_space()

constexpr bool genesis::utils::is_space ( char  c )

constexprnoexcept

Return whether a char is some form of white space charater, so either space, tab, new line, carriage return, form feed, or vertical tab.

Definition at line 200 of file char.hpp.

is_square()

bool genesis::utils::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.

Definition at line 178 of file utils/containers/matrix/operators.hpp.

is_strict_subset()

bool is_strict_subset	(	Bitvector const &	sub,
		Bitvector const &	super
	)

Strict subset.

Definition at line 94 of file utils/math/bitvector/operators.cpp.

is_strict_superset()

bool is_strict_superset	(	Bitvector const &	super,
		Bitvector const &	sub
	)

Strict superset.

Definition at line 102 of file utils/math/bitvector/operators.cpp.

is_subset()

bool is_subset	(	Bitvector const &	sub,
		Bitvector const &	super
	)

Subset or equal.

Definition at line 107 of file utils/math/bitvector/operators.cpp.

is_superset()

bool is_superset	(	Bitvector const &	super,
		Bitvector const &	sub
	)

Superset or equal.

Definition at line 112 of file utils/math/bitvector/operators.cpp.

is_symmetric()

bool genesis::utils::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.

Definition at line 188 of file utils/containers/matrix/operators.hpp.

is_upper()

constexpr bool genesis::utils::is_upper ( char  c )

constexprnoexcept

Return whether a char is an upper case letter (A-Z), ASCII-only.

Definition at line 125 of file char.hpp.

is_valid_filename()

bool is_valid_filename

(

std::string const &

filename

)

Check whether a file name is valid.

Validating filenames depends on the operating system and file system of the disk. Thus, this is usually not an easy task. This function only checks some basics and is meant to catch the most common problems.

The function is meant to be called on the file name itself, without the directory path leading to it. File extensions are allowed. Thus, you might need to call file_basename() before in order to get the file name without the path.

Invalid filenames are:

• Those with spaces at the beginning or end, or only consisting of spaces (or empty).
• Those which contain any of the chars < > : " \ / | ? *.
• Those which contain any non-printable character, as determined via isprint().

This might be too converative for some system, or allow too much for others. It however should return true for filenames that work on most systems.

Definition at line 835 of file fs.cpp.

is_valid_int_pow()

bool genesis::utils::is_valid_int_pow ( size_t  base, size_t  exp  )

inline

Return whether the given power can be stored within a size_t.

Use int_pow() to calculate the actual value of the power.

Definition at line 211 of file common.hpp.

is_xdigit()

constexpr bool genesis::utils::is_xdigit ( char  c )

constexprnoexcept

Return whether a char is a hexadecimal digit (0-9 or A-F or a-f), ASCII-only.

Definition at line 105 of file char.hpp.

iterate_deletions()

utils::Range< IteratorDeletions > genesis::utils::iterate_deletions ( TwobitVector const &  vector )

inline

Definition at line 220 of file iterator_deletions.hpp.

iterate_insertions()

utils::Range< IteratorInsertions > genesis::utils::iterate_insertions ( TwobitVector const &  vector )

inline

Definition at line 249 of file iterator_insertions.hpp.

iterate_substitutions()

utils::Range< IteratorSubstitutions > genesis::utils::iterate_substitutions ( TwobitVector const &  vector )

inline

Definition at line 239 of file iterator_substitutions.hpp.

join() [1/5]

std::string genesis::utils::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.

Definition at line 740 of file string.hpp.

join() [2/5]

Interval<DataType, NumericalType, IntervalKind> genesis::utils::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.

The data of the newly created interval is default constructed.

Definition at line 127 of file utils/containers/interval_tree/functions.hpp.

join() [3/5]

Interval<DataType, NumericalType, IntervalKind> genesis::utils::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.

The provided data is moved to the new Interval.

Definition at line 162 of file utils/containers/interval_tree/functions.hpp.

join() [4/5]

Interval<DataType, NumericalType, IntervalKind> genesis::utils::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.

The provided data is copied to the new Interval.

Definition at line 144 of file utils/containers/interval_tree/functions.hpp.

join() [5/5]

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.

Print elements of the given container to the output stream, joining them with the delimiter, for a container of signed or unsigned char.

The delimiter is only printed in between elements, but not after the last. The container is iterated via its range based for loop, thus it needs to have begin() and end() functions. For turning the elements of the container into a string, their operator << is used. Thus, this function can used with all types that support this operator.

We need this specialization, as the unsigned chars are otherwise turned into their char (ASCII) equivalent, which we do not want. Instead, we want to output them here as plain numbers.

Definition at line 699 of file string.hpp.

kendalls_tau_correlation_coefficient() [1/2]

double genesis::utils::kendalls_tau_correlation_coefficient	(	InputIteratorA	first_a,
		InputIteratorA	last_a,
		InputIteratorB	first_b,
		InputIteratorB	last_b,
		KendallsTauMethod	method = KendallsTauMethod::kTauB
	)

This function computes Kendall's tau, if requested accounting for ties, and using Knight's algorithm for speed.

Knight, W. (1966). "A Computer Method for Calculating Kendall's Tau with Ungrouped Data". Journal of the American Statistical Association. 61 (314): 436–439. doi:10.2307/2282833. JSTOR 2282833.

See kendalls_tau_correlation_coefficient_naive() for the naive, slow version.

Definition at line 229 of file correlation.hpp.

kendalls_tau_correlation_coefficient() [2/2]

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.

This function computes Kendall's tau, if requested accounting for ties, and using Knight's algorithm for speed.

Knight, W. (1966). "A Computer Method for Calculating Kendall's Tau with Ungrouped Data". Journal of the American Statistical Association. 61 (314): 436–439. doi:10.2307/2282833. JSTOR 2282833.

See kendalls_tau_correlation_coefficient_naive() for the naive, slow version.

Definition at line 423 of file correlation.cpp.

kendalls_tau_correlation_coefficient_clean_()

double genesis::utils::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.

Definition at line 359 of file correlation.cpp.

kendalls_tau_correlation_coefficient_naive()

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.

This version uses a naive nested loop over the elements. It is mainly provided for testing the more advanced implementation, see kendalls_tau_correlation_coefficient() for details.

Definition at line 468 of file correlation.cpp.

kendalls_tau_count_tau_c_m_()

size_t genesis::utils::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.

Definition at line 55 of file correlation.cpp.

kendalls_tau_count_ties_()

size_t genesis::utils::kendalls_tau_count_ties_

(

std::vector< T > const &

values

)

Helper function to count the number of tied pairs induced by equal values.

Definition at line 230 of file correlation.cpp.

kendalls_tau_count_ties_sorted_()

size_t genesis::utils::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.

Definition at line 254 of file correlation.cpp.

kendalls_tau_count_ties_sorted_pairs_rank_()

size_t genesis::utils::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.

Definition at line 325 of file correlation.cpp.

kendalls_tau_count_ties_sorted_rank_()

size_t genesis::utils::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.

Definition at line 291 of file correlation.cpp.

kendalls_tau_merge_count_()

size_t genesis::utils::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.

Definition at line 152 of file correlation.cpp.

kendalls_tau_method_()

double genesis::utils::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.

We take all values as inputs, as in the presence of nan values, these better be computed correclty by the two algorithms directly, instead of inferring, e.g., n from the list size...

Definition at line 80 of file correlation.cpp.

kendalls_tau_sort_and_count_()

size_t genesis::utils::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.

Definition at line 191 of file correlation.cpp.

log_binomial_coefficient()

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.

See binomial_coefficient() for details. This function here is used in the internal computatation, and offered for cases where working with binomials in log space is more convenient due to the handling of numbers with very large and very small exponents, such as in binomial_distribution().

Definition at line 497 of file binomial.cpp.

log_binomial_distribution()

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.

See binomial_distribution() for details.

Definition at line 519 of file binomial.cpp.

log_factorial()

double log_factorial

(

size_t

n

)

Return the logarithm (base e) of the factorial of n, that is log(n!).

This is implemented via a precise lookup table for n < 1024, and uses Stirling's approximation for larger values, with a slight error in the order of less than 1/(360 * n^3), that is, less than 2.59e-12 for all n >= 1024. See https://www.johndcook.com/blog/2010/08/16/how-to-compute-log-factorial/ for details.

Definition at line 445 of file binomial.cpp.

log_factorial_lookup_generator_()

std::vector<double> genesis::utils::log_factorial_lookup_generator_

(

)

Helper function to generate above lookup table.

The function is not called from anywhere, but kept here for reference, in case we want to modify the above lookup table. Computes log(x!), which we do neatly in an iterative way: x! = (x-1)! * x ==> log(x!) = log((x-1)!) + log(x) See https://stackoverflow.com/a/37715980/4184258

Definition at line 386 of file binomial.cpp.

logging_progress_value()

long genesis::utils::logging_progress_value ( long  value = -1 )

inline

Hack function to make sure that the value arugment in LOG_PROG is only evaluated once.

Without this function, LOG_PROG would include two appearances of its variable value, which means that a statement like

LOG_PROG(++i, n) << "of progress.";

would lead to a double evaluation of the increment statement ++i. That is not intended, thus we need this hack function.

Definition at line 179 of file logging.hpp.

make_bool_vector_from_indices()

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.

The function expectes a list of indices. It returns a bool vector with the size of the largest index, or the provided size (if set to a value > 0), where all positions of these indices are true, and all other positions are false.

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

make_filter_iterator()

FilterIterator<PredicateFunctor, BaseIterator> genesis::utils::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.

Caveat: Note that by default, we use a default-constructed end iterator. This only works for containers where the default-constructed iterator is the end iterator! In particular, this does NOT work for many STL containers. For example, for a std::vector, one needs to explicitly use vector.end() here.

This constructor needs to be used for both the begin and end of the range that one wants to iterate, using the same filter function both times. See also make_filter_iterator() and make_filter_range() for helper functions to easily create an instance.

Definition at line 272 of file filter_iterator.hpp.

make_filter_range() [1/3]

Range<FilterIterator<PredicateFunctor, BaseIterator> > genesis::utils::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.

Definition at line 285 of file filter_iterator.hpp.

make_filter_range() [2/3]

Range<FilterIterator<PredicateFunctor, typename Container::iterator> > genesis::utils::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.

Definition at line 301 of file filter_iterator.hpp.

make_filter_range() [3/3]

Range<FilterIterator<PredicateFunctor, typename Container::const_iterator> > genesis::utils::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.

Definition at line 320 of file filter_iterator.hpp.

make_heatmap_color_norm()

std::unique_ptr< ColorNormalization > make_heatmap_color_norm	(	Matrix< double > const &	values,
		HeatmapParameters const &	parameters
	)

Definition at line 158 of file heat_map.cpp.

make_heatmap_matrix()

Matrix< Color > make_heatmap_matrix	(	Matrix< double > const &	values,
		HeatmapParameters const &	parameters
	)

Definition at line 189 of file heat_map.cpp.

make_optional()

Optional<T> genesis::utils::make_optional ( T const &  v )

inline

Convenience function to create an Optional.

Definition at line 575 of file optional.hpp.

make_safe_interval() [1/3]

Interval<DataType, NumericalType, IntervalKind> genesis::utils::make_safe_interval	(	NumericalType	lhs,
		NumericalType	rhs
	)

Creates a safe Interval that puts the lower bound left automatically.

The data of the newly created interval is default constructed.

Definition at line 58 of file utils/containers/interval_tree/functions.hpp.

make_safe_interval() [2/3]

Interval<DataType, NumericalType, IntervalKind> genesis::utils::make_safe_interval	(	NumericalType	lhs,
		NumericalType	rhs,
		DataType &&	data
	)

Creates a safe Interval that puts the lower bound left automatically.

The provided data is moved to the new Interval.

Definition at line 103 of file utils/containers/interval_tree/functions.hpp.

make_safe_interval() [3/3]

Interval<DataType, NumericalType, IntervalKind> genesis::utils::make_safe_interval	(	NumericalType	lhs,
		NumericalType	rhs,
		DataType const &	data
	)

Creates a safe Interval that puts the lower bound left automatically.

The provided data is copied to the new Interval.

Definition at line 80 of file utils/containers/interval_tree/functions.hpp.

make_svg_axis() [1/2]

SvgGroup make_svg_axis	(	SvgAxisSettings const &	settings,
		std::map< double, std::string > const &	labels,
		std::string const &	name = ""
	)

Simple helper to make an axis.

The helper currently only draws lines and puts the labels alongside. The given labels have already to be pre-computed, with their position (first of the map) being their relative position in [ 0.0, 1.0 ] along the axis.

Definition at line 52 of file axis.cpp.

make_svg_axis() [2/2]

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.

This overload of the function takes the result of the Tickmarks class when creating labels, and forwards it to the other overload that takes string labeles instead, for convenience. When using round_labels (default true), std::round is called on the label values first, in order to print integer numbers.

Definition at line 202 of file axis.cpp.

make_svg_color_bar()

std::pair< SvgGradientLinear, SvgGroup > make_svg_color_bar	(	SvgColorBarSettings const &	settings,
		ColorMap const &	map,
		ColorNormalization const &	norm,
		std::string const &	id
	)

Definition at line 325 of file color_bar.cpp.

make_svg_color_bar_discrete_()

static std::pair<SvgGradientLinear, SvgGroup> genesis::utils::make_svg_color_bar_discrete_ ( SvgColorBarSettings const &  settings, std::map< double, Color > const &  stops  )

static

Definition at line 128 of file color_bar.cpp.

make_svg_color_bar_gradient_()

static std::pair<SvgGradientLinear, SvgGroup> genesis::utils::make_svg_color_bar_gradient_ ( SvgColorBarSettings const &  settings, ColorMap const &  map, ColorNormalization const &  norm, std::string const &  id  )

static

Definition at line 64 of file color_bar.cpp.

make_svg_color_bar_tickmarks_()

static void genesis::utils::make_svg_color_bar_tickmarks_ ( SvgColorBarSettings const &  settings, ColorMap const &  map, ColorNormalization const &  norm, SvgGroup &  group  )

static

Definition at line 210 of file color_bar.cpp.

make_svg_color_list() [1/2]

SvgGroup make_svg_color_list	(	ColorMap const &	map,
		std::vector< std::string > const &	labels
	)

Definition at line 376 of file color_bar.cpp.

make_svg_color_list() [2/2]

SvgGroup make_svg_color_list	(	std::vector< Color > const &	colors,
		std::vector< std::string > const &	labels
	)

Definition at line 389 of file color_bar.cpp.

make_svg_color_list_entry_()

void genesis::utils::make_svg_color_list_entry_	(	size_t	i,
		Color const &	color,
		std::string const &	label,
		SvgGroup &	group
	)

Definition at line 366 of file color_bar.cpp.

make_svg_matrix() [1/3]

SvgGroup make_svg_matrix	(	Matrix< Color > const &	mat,
		SvgMatrixSettings	settings
	)

Definition at line 147 of file formats/svg/matrix.cpp.

make_svg_matrix() [2/3]

SvgGroup make_svg_matrix	(	Matrix< Color > const &	mat,
		SvgMatrixSettings	settings,
		std::vector< std::string > const &	row_labels
	)

Definition at line 137 of file formats/svg/matrix.cpp.

make_svg_matrix() [3/3]

SvgGroup make_svg_matrix	(	Matrix< Color > const &	mat,
		SvgMatrixSettings	settings,
		std::vector< std::string > const &	row_labels,
		std::vector< std::string > const &	col_labels
	)

Definition at line 50 of file formats/svg/matrix.cpp.

make_svg_pie_chart()

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.

The given values are automatically re-scaled to fill the circle. If there are more colors than values, only the first ones needed are used; if given colors have fewer entries thatn there are values, an exception is thrown.

The radius of the char defaults to 1.0, and the start_angle to -pi/2, so that the chart starts from the top (most typical). By default, we also draw the values clockwise (that is, reversed form the mathematical direction).

Definition at line 51 of file pie_chart.cpp.

make_transform_iterator()

TransformIterator<TransformFunctor, BaseIterator> genesis::utils::make_transform_iterator	(	TransformFunctor	unary_func,
		BaseIterator	iterator
	)

Construct a transforming iterator, given the underlying base iterator and the transformation function.

This constructor needs to be used for both the begin and end of the range that one wants to iterate, using the same transformation function both times. See also make_transform_iterator() and make_transform_range() for helper functions to easily create an instance.

Definition at line 426 of file transform_iterator.hpp.

make_transform_range() [1/3]

Range<TransformIterator<TransformFunctor, BaseIterator> > genesis::utils::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.

Definition at line 438 of file transform_iterator.hpp.

make_transform_range() [2/3]

Range<TransformIterator<TransformFunctor, typename Container::iterator> > genesis::utils::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.

Definition at line 454 of file transform_iterator.hpp.

make_transform_range() [3/3]

Range<TransformIterator<TransformFunctor, typename Container::const_iterator> > genesis::utils::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.

Definition at line 473 of file transform_iterator.hpp.

make_unique()

std::unique_ptr<T> genesis::utils::make_unique

(

Args &&...

args

)

Returns a std::unique_ptr for a given type.

Since this is not available in C++11, we need our own implementation. It is following http://herbsutter.com/gotw/_102/ When using this function, make sure to specify at least the utils namespace, even from within that namespace, in order to avoid name overloads if compiled with C++17.

Definition at line 82 of file std.hpp.

manhattan_distance() [1/2]

double genesis::utils::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.

The function is a more expressive version of p_norm_distance( ForwardIteratorA, ForwardIteratorA, ForwardIteratorB, ForwardIteratorB, double ) with p == 1.0. See there for details.

Definition at line 353 of file distance.hpp.

manhattan_distance() [2/2]

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

inline

Calculate the Manhattan norm (L1 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 == 1.0. See there for details.

Definition at line 367 of file distance.hpp.

manhattan_distance_matrix()

Matrix< double > manhattan_distance_matrix

(

Matrix< double > const &

data

)

Calculate the pairwise manhatten distance matrix between the rows of a given matrix.

See p_norm_distance_matrix() for details. This function simply uses a fixed p == 1.0 for more expressive code.

Definition at line 105 of file distance.cpp.

manhattan_norm() [1/2]

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

Calculate the Manhattan norm (L1 norm) of a range of numbers.

The function is a more expressive version of p_norm( ForwardIterator, ForwardIterator, double ) with p == 1.0. See there for details.

Definition at line 131 of file distance.hpp.

manhattan_norm() [2/2]

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

inline

Calculate the Manhattan norm (L1 norm) of a std::vector of double elements.

The function is a more expressive version of p_norm( std::vector<double> const&, double ) with p == 1.0. See there for details.

Definition at line 142 of file distance.hpp.

match_wildcards()

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.

Definition at line 286 of file string.cpp.

matrix_addition() [1/2]

Matrix<T> genesis::utils::matrix_addition	(	Matrix< A > const &	a,
		Matrix< B > const &	b
	)

Calculate the element-wise sum of two Matrices.

The two matrices need to have the same dimensions.

Definition at line 486 of file math/matrix.hpp.

matrix_addition() [2/2]

Matrix<T> genesis::utils::matrix_addition	(	Matrix< A > const &	matrix,
		B const &	scalar
	)

Calculate the element-wise sum of a Matrix and a scalar.

Definition at line 505 of file math/matrix.hpp.

matrix_col_minmax()

std::vector<MinMaxPair<T> > genesis::utils::matrix_col_minmax	(	Matrix< T > const &	data,
		bool	ignore_non_finite_values = true
	)

Calculate the column-wise min and max values of a Matrix.

If ignore_non_finite_values is true (default), non-finite values are ignored. See also matrix_row_minmax() and matrix_minmax().

Definition at line 99 of file math/matrix.hpp.

matrix_col_sums()

std::vector<T> genesis::utils::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.

If ignore_non_finite_values is true (default), non-finite values are ignored. See also matrix_row_sums() and matrix_sum().

Definition at line 231 of file math/matrix.hpp.

matrix_minmax()

MinMaxPair<T> genesis::utils::matrix_minmax	(	Matrix< T > const &	data,
		bool	ignore_non_finite_values = true
	)

Calculate the min and max values of a Matrix.

If ignore_non_finite_values is true (default), non-finite values are ignored. See also matrix_col_minmax() and matrix_row_minmax().

Definition at line 55 of file math/matrix.hpp.

matrix_multiplication() [1/4]

Matrix<T> genesis::utils::matrix_multiplication	(	Matrix< A > const &	a,
		Matrix< B > const &	b
	)

Calculate the product of two Matrices.

The two matrices need to have fitting dimensions, i.e., a[ l, m ] x b[ m, n ], which results in a Matrix of dimensions r[ l, n ].

Definition at line 548 of file math/matrix.hpp.

matrix_multiplication() [2/4]

std::vector<T> genesis::utils::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.

Thus, the two arguments need to have fitting dimensions, i.e., a[ l, m ] x b[ m ]. The resulting vector has size l, which represent the rows of the result Matrix.

Definition at line 602 of file math/matrix.hpp.

matrix_multiplication() [3/4]

Matrix<T> genesis::utils::matrix_multiplication	(	Matrix< A > const &	matrix,
		B const &	scalar
	)

Calculate the element-wise multiplication of a Matrix and a scalar.

Definition at line 622 of file math/matrix.hpp.

matrix_multiplication() [4/4]

std::vector<T> genesis::utils::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.

Thus, the two arguments need to have fitting dimensions, i.e., a[ m ] x b[ m, n ]. The resulting vector has size n, which represent the columns of the result Matrix.

Definition at line 578 of file math/matrix.hpp.

matrix_row_minmax()

std::vector<MinMaxPair<T> > genesis::utils::matrix_row_minmax	(	Matrix< T > const &	data,
		bool	ignore_non_finite_values = true
	)

Calculate the row-wise min and max values of a Matrix.

If ignore_non_finite_values is true (default), non-finite values are ignored. See also matrix_col_minmax() and matrix_minmax().

Definition at line 145 of file math/matrix.hpp.

matrix_row_sums()

std::vector<T> genesis::utils::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.

If ignore_non_finite_values is true (default), non-finite values are ignored. See also matrix_col_sums() and matrix_sum().

Definition at line 209 of file math/matrix.hpp.

matrix_sort_by_col_sum_symmetric()

Matrix<T> genesis::utils::matrix_sort_by_col_sum_symmetric

(

Matrix< T > const &

data

)

Sort rows and columns of a Matrix by the sum or the columns.

This is an operation for square matrices: It takes the row sum as sorting criterion, and sorts the rows and the columns according to that order. This is mostly useful for symmetric matrices, where m[ i, j ] == m[ j, i ]. In those cases, the sorting is stable with respect to the symmetry.

See also matrix_sort_by_row_sum_symmetric(). In case of symmetric matrices, it should yield the same Matrix.

Definition at line 415 of file math/matrix.hpp.

matrix_sort_by_row_sum_symmetric()

Matrix<T> genesis::utils::matrix_sort_by_row_sum_symmetric

(

Matrix< T > const &

data

)

Sort rows and columns of a Matrix by the sum or the rows.

This is an operation for square matrices: It takes the row sum as sorting criterion, and sorts the rows and the columns according to that order. This is mostly useful for symmetric matrices, where m[ i, j ] == m[ j, i ]. In those cases, the sorting is stable with respect to the symmetry.

See also matrix_sort_by_col_sum_symmetric(). In case of symmetric matrices, it should yield the same Matrix.

Definition at line 384 of file math/matrix.hpp.

matrix_sort_diagonal_symmetric()

Matrix<T> genesis::utils::matrix_sort_diagonal_symmetric

(

Matrix< T > const &

data

)

Sort a Matrix so that the highest entries are on the diagonal.

The Matrix is sorted by moving the row and col with the highest entry to [ 0, 0 ], and then applying this operation to the rest of the matrix (that is, excluding the first row and col) iteratievly. The Matrix does not have to be symmetrical, but sorting keeps rows and columns intact.

Definition at line 443 of file math/matrix.hpp.

matrix_subtraction()

Matrix<T> genesis::utils::matrix_subtraction	(	Matrix< A > const &	a,
		Matrix< B > const &	b
	)

Calculate the element-wise difference of two Matrices.

The two matrices need to have the same dimensions.

Definition at line 522 of file math/matrix.hpp.

matrix_sum()

T genesis::utils::matrix_sum	(	Matrix< T > const &	data,
		bool	ignore_non_finite_values = true
	)

Calculate the sum of all elements in a Matrix.

If ignore_non_finite_values is true (default), non-finite values are ignored. See also matrix_col_sums() and matrix_row_sums().

Definition at line 190 of file math/matrix.hpp.

max_bin()

size_t max_bin

(

const Histogram &

h

)

Definition at line 63 of file utils/math/histogram/stats.cpp.

max_value()

double max_value

(

const Histogram &

h

)

Definition at line 53 of file utils/math/histogram/stats.cpp.

maximum_distance() [1/2]

double genesis::utils::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.

The function is a more expressive version of p_norm_distance( ForwardIteratorA, ForwardIteratorA, ForwardIteratorB, ForwardIteratorB, double ) with p == std::numeric_limits<double>::infinity(). See there for details.

Definition at line 410 of file distance.hpp.

maximum_distance() [2/2]

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

inline

Calculate the Maximum norm (infinity 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 == std::numeric_limits<double>::infinity(). See there for details.

Definition at line 428 of file distance.hpp.

maximum_distance_matrix()

Matrix< double > maximum_distance_matrix

(

Matrix< double > const &

data

)

Calculate the pairwise maximum distance matrix between the rows of a given matrix.

See p_norm_distance_matrix() for details. This function simply uses a fixed p == std::numeric_limits<double>::infinity() more expressive code.

Definition at line 115 of file distance.cpp.

maximum_norm() [1/2]

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

Calculate the Maximum norm (infinity norm) of a range of numbers.

The function is a more expressive version of p_norm( ForwardIterator, ForwardIterator, double ) with p == std::numeric_limits<double>::infinity(). See there for details.

Definition at line 178 of file distance.hpp.

maximum_norm() [2/2]

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

inline

Calculate the Maximum norm (infinity norm) of a std::vector of double elements.

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

Definition at line 190 of file distance.hpp.

mean()

double mean

(

const Histogram &

h

)

Compute the bin-weighted arithmetic mean.

The histogram is regarded as a probability distribution. Negative bin values are ignored for the purposes of this calculation. The accuracy of the result is limited by the bin width.

Definition at line 91 of file utils/math/histogram/stats.cpp.

mean_squared_error()

double genesis::utils::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.

The error per data point (x,y) is calculated as the squared differences between y and the prediction given by the linear function lin_fct for x. The function returns the mean of the errors for all data points.

See also

simple_linear_regression() for calculating such a fit.

Definition at line 125 of file slr.hpp.

mean_stddev() [1/2]

MeanStddevPair genesis::utils::mean_stddev	(	ForwardIterator	first,
		ForwardIterator	last,
		double	epsilon = -1.0
	)

Calculate the arithmetic mean and standard deviation of a range of double elements.

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 and standard deviation of all finite elements in the range. If no elements are finite, or if the range is empty, both returned values are 0.0. Non-finite numbers are ignored.

If the resulting standard deviation is below the given epsilon (e.g, 0.0000001), it is "corrected" to be 1.0 instead. This is an inelegant (but usual) way to handle near-zero values, which for some use cases would cause problems like a division by zero later on. By default, epsilon is -1.0, which deactivates this check.

See also

mean_stddev( std::vector<double> const&, double epsilon ) for a version for std::vector.

arithmetic_mean() for a function that only calculates the mean, and thus saves the effort of a second iteration over the range.

Definition at line 358 of file statistics.hpp.

mean_stddev() [2/2]

MeanStddevPair genesis::utils::mean_stddev ( std::vector< double > const &  vec, double  epsilon = -1.0  )

inline

Calculate the mean and standard deviation of a std::vector of double elements.

See also

mean_stddev( ForwardIterator first, ForwardIterator last, double epsilon ) for details.

arithmetic_mean() for a function that only calculates the mean, and thus saves the effort of a second iteration over the range.

Definition at line 413 of file statistics.hpp.

median() [1/3]

double median

(

const Histogram &

h

)

Definition at line 68 of file utils/math/histogram/stats.cpp.

median() [2/3]

double genesis::utils::median	(	RandomAccessIterator	first,
		RandomAccessIterator	last
	)

Calculate the median value of a sorted range of double values.

The iterators are as usual: first points to the first element of the range, last to the past-the-end element.

The median of an odd sized range is its middle element; the median of an even sized range is the arithmetic mean (average) of its two middle elements.

Definition at line 1014 of file statistics.hpp.

median() [3/3]

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

inline

Calculate the median value of a vector of double.

The vector has to be sorted.

Definition at line 1050 of file statistics.hpp.

min_bin()

size_t min_bin

(

const Histogram &

h

)

Definition at line 58 of file utils/math/histogram/stats.cpp.

min_value()

double min_value

(

const Histogram &

h

)

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

minimal_layout()

TableLayout minimal_layout

(

)

Definition at line 439 of file utils/text/table.cpp.

minmax_value() [1/2]

std::pair<T, T> genesis::utils::minmax_value	(	T const &	a,
		T const &	b
	)

Returns the lowest and the greatest of the given values, by value.

The function differs from std::minmax in its return value. Instead of references, it returns by value, which is useful for integers and the like.

Definition at line 128 of file algorithm.hpp.

minmax_value() [2/2]

std::pair<T, T> genesis::utils::minmax_value	(	T const &	a,
		T const &	b,
		Compare	comp
	)

Returns the lowest and the greatest of the given values, by value.

The function differs from std::minmax in its return value. Instead of references, it returns by value, which is useful for integers and the like.

Definition at line 137 of file algorithm.hpp.

mode_to_string_()

static std::string genesis::utils::mode_to_string_ ( std::ios_base::openmode  mode )

static

Definition at line 120 of file strict_fstream.cpp.

multi_dimensional_scaling() [1/2]

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).

The function expectes a square distances matrix as well as a set of initial embedding values. See multi_dimensional_scaling() for a version that uses randomly initialized embedding values. The function then runs multi-dimensional scaling (MDS) for a given number of dimensions, and optimizes the embeddings in iterations. It offers two choices for the MDS algorithm, of which we recommend the default one, see MdsAlgorithm.

The implementation is based on the SimpleMatrix library by Quan Wang, with his explicit permission to use this code here. The copyright (C) of the implementation is held by Quan Wang, 2013. We adapted the implementation to our Matrix class and changed the error reporting mechanism to exceptions. For further details, see the Acknowledgements.

Definition at line 262 of file mds.cpp.

multi_dimensional_scaling() [2/2]

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).

Run MDS with randomly initialized embedding values.

See also

multi_dimensional_scaling() for details on the function, its parameters, and the license of the implementation.

Definition at line 231 of file mds.cpp.

multi_dimensional_scaling_smacof()

static Matrix<double> genesis::utils::multi_dimensional_scaling_smacof ( Matrix< double > const &  distances, Matrix< double > const &  initial_values, size_t  dimensions, size_t  iterations  )

static

Definition at line 155 of file mds.cpp.

multi_dimensional_scaling_ucf()

static Matrix<double> genesis::utils::multi_dimensional_scaling_ucf ( Matrix< double > const &  distances, Matrix< double > const &  initial_values, size_t  dimensions, size_t  iterations  )

static

Definition at line 63 of file mds.cpp.

multinomial_distribution() [1/2]

std::vector< size_t > multinomial_distribution	(	std::vector< double > const &	p,
		size_t	n
	)

Select a random sample following a multinomial distribution.

This overload accepts a std::vector<double>, and checks that all values are finite and non-negative. Otherwise the same.

Definition at line 158 of file distribution.cpp.

multinomial_distribution() [2/2]

std::vector< size_t > multinomial_distribution	(	std::vector< size_t > const &	p,
		size_t	n
	)

Select a random sample following a multinomial distribution.

This function computes a random sample formed by n trials from an underlying distribution p. The values in have to be non-negative, and are taken as weights of each category; they do not need to be normalized to sum to 1. The function models drawing from multiple categories, each with probability as given in p, with replacement. See multivariate_hypergeometric_distribution() for the equivalent distribution to draw without replacement instead.

See https://en.wikipedia.org/wiki/Multinomial_distribution for a description of the distribution. See https://www.gnu.org/software/gsl/doc/html/randist.html#the-multinomial-distribution for details on the distribution and the used algorithm, which follows C.S. Davis, "The computer generation of multinomial random variates", Comp. Stat. Data Anal. 16 (1993) 205–217.

Definition at line 153 of file distribution.cpp.

multinomial_distribution_()

std::vector<size_t> genesis::utils::multinomial_distribution_	(	std::vector< T > const &	p,
		size_t	n
	)

Definition at line 114 of file distribution.cpp.

multivariate_hypergeometric_distribution()

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.

This function computes a random sample formed by n trials from an underlying distribution p. The values in have to be non-negative, and are taken as weights of each category; they do not need to be normalized to sum to 1. The function models drawing from multiple categories, each with weights as given in p, without replacement. See multinomial_distribution() for the equivalent distribution to draw with replacement instead.

Definition at line 517 of file distribution.cpp.

n_first_elements()

std::vector<T> genesis::utils::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.

The function uses comp for the comparison, and returns a vector of the first n elements of the input as sorted by comp, in their correct order. For instance, when using std::greater, the largest n elements are returned, with the largest one first, decending after that.

Definition at line 342 of file ranking.hpp.

normalize()

void normalize	(	Histogram &	h,
		double	total
	)

Definition at line 61 of file operations.cpp.

normalize_cols()

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 ].

The Matrix is manipulated inline. For each column, the new values of the Matrix are calculated as \( x_{new} = \frac{ x - x_{min} }{ x_{max} - x_{min} } \).

The function returns a vector containing the min and max values of the columns before normalization, see matrix_col_minmax().

Parameters

data	Input data Matrix; normalization is done inline.

Returns

Vector containing the min and max values for each column before normalization.

Definition at line 52 of file math/matrix.cpp.

normalize_rows()

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 ].

The Matrix is manipulated inline. For each row, the new values of the Matrix are calculated as \( x_{new} = \frac{ x - x_{min} }{ x_{max} - x_{min} } \).

The function returns a vector containing the min and max values of the rows before normalization, see matrix_row_minmax().

Parameters

data	Input data Matrix; normalization is done inline.

Returns

Vector containing the min and max values for each row before normalization.

Definition at line 71 of file math/matrix.cpp.

offset()

void offset	(	Histogram &	h,
		double	value
	)

Definition at line 47 of file operations.cpp.

operator!=() [1/10]

bool genesis::utils::operator!= ( Color const &  lhs, Color const &  rhs  )

inline

Definition at line 224 of file color.hpp.

operator!=() [2/10]

bool genesis::utils::operator!=	(	JsonDocument const &	lhs,
		JsonDocument const &	rhs
	)

operator!=() [3/10]

bool genesis::utils::operator!=	(	JsonDocument const &	v,
		std::nullptr_t
	)

operator!=() [4/10]

bool genesis::utils::operator!=	(	NexusTaxa const &	lhs,
		NexusTaxa const &	rhs
	)

Definition at line 105 of file taxa.hpp.

operator!=() [5/10]

bool genesis::utils::operator!= ( nullopt_t  , Optional< T > const &  x  )

inline

Definition at line 432 of file optional.hpp.

operator!=() [6/10]

bool genesis::utils::operator!= ( Optional< T > const &  x, nullopt_t    )

inline

Definition at line 426 of file optional.hpp.

operator!=() [7/10]

bool genesis::utils::operator!= ( Optional< T > const &  x, Optional< U > const &  y  )

inline

Definition at line 380 of file optional.hpp.

operator!=() [8/10]

bool genesis::utils::operator!= ( Optional< T > const &  x, U const &  v  )

inline

Definition at line 502 of file optional.hpp.

operator!=() [9/10]

bool genesis::utils::operator!=	(	std::nullptr_t	,
		JsonDocument const &	v
	)

operator!=() [10/10]

bool genesis::utils::operator!= ( U const &  v, Optional< T > const &  x  )

inline

Definition at line 508 of file optional.hpp.

operator&() [1/2]

Bitvector genesis::utils::operator&	(	Bitvector const &	lhs,
		Bitvector const &	rhs
	)

Definition at line 271 of file bitvector.cpp.

operator&() [2/2]

constexpr bool genesis::utils::operator& ( SkipWhitespace  lhs, SkipWhitespace  rhs  )

inlineconstexprnoexcept

And-operator to check whether a SkipWhitespace is set.

Typical usage:

SkipWhitespace option;
if( option & SkipWhitespace::kTrailing ) {
    // Do stuff...
}

See SkipWhitespace for more information.

Definition at line 97 of file scanner.hpp.

operator<() [1/8]

bool genesis::utils::operator<	(	const JsonDocument::ValueType	lhs,
		const JsonDocument::ValueType	rhs
	)

Returns an ordering that is similar to Python:

• order: null < boolean < number < object < array < string
• furthermore, each type is not smaller than itself %

Definition at line 859 of file json/document.cpp.

operator<() [2/8]

bool genesis::utils::operator<	(	JsonDocument const &	lhs,
		JsonDocument const &	rhs
	)

operator<() [3/8]

bool genesis::utils::operator<	(	JsonDocument::const_reference	lhs,
		JsonDocument::const_reference	rhs
	)

Compares whether one JSON value lhs is less than another JSON value rhs according to the following rules:

• If lhs and rhs have the same type, the values are compared using the default < operator.
• Integer and floating-point numbers are automatically converted before comparison
• In case lhs and rhs have different types, the values are ignored and the order of the types is considered, see operator<(const JsonDocument::ValueType, const JsonDocument::ValueType). %

Definition at line 793 of file json/document.cpp.

operator<() [4/8]

bool genesis::utils::operator< ( nullopt_t  , Optional< T > const &  x  )

inline

Definition at line 444 of file optional.hpp.

operator<() [5/8]

bool genesis::utils::operator< ( Optional< T > const &  , nullopt_t    )

inline

Definition at line 438 of file optional.hpp.

operator<() [6/8]

bool genesis::utils::operator< ( Optional< T > const &  x, Optional< U > const &  y  )

inline

Definition at line 386 of file optional.hpp.

operator<() [7/8]

bool genesis::utils::operator< ( Optional< T > const &  x, U const &  v  )

inline

Definition at line 514 of file optional.hpp.

operator<() [8/8]

bool genesis::utils::operator< ( U const &  v, Optional< T > const &  x  )

inline

Definition at line 520 of file optional.hpp.

operator<<() [1/12]

std::ostream & operator<<	(	std::ostream &	os,
		Color const &	color
	)

Write a textual representation of the Color the a stream, in the format "(r, g, b, a)".

Definition at line 129 of file utils/color/functions.cpp.

operator<<() [2/12]

std::ostream & operator<<	(	std::ostream &	os,
		const Histogram &	h
	)

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

operator<<() [3/12]

std::ostream & operator<<	(	std::ostream &	os,
		const HistogramAccumulator &	h
	)

Definition at line 59 of file utils/math/histogram/operators.cpp.

operator<<() [4/12]

std::ostream & operator<<	(	std::ostream &	os,
		const Matrix< signed char > &	matrix
	)

Template specialization for signed char, in order to print nicely.

Definition at line 89 of file utils/containers/matrix/operators.cpp.

operator<<() [5/12]

std::ostream& genesis::utils::operator<<	(	std::ostream &	os,
		const Matrix< T > &	matrix
	)

Print the elements of a Matrix to a stream, using operator << for each element.

Definition at line 211 of file utils/containers/matrix/operators.hpp.

operator<<() [6/12]

std::ostream & operator<<	(	std::ostream &	os,
		const Matrix< unsigned char > &	matrix
	)

Template specialization for unsigned char, in order to print nicely.

Definition at line 96 of file utils/containers/matrix/operators.cpp.

operator<<() [7/12]

std::ostream & operator<<	(	std::ostream &	os,
		GeoCoordinate const &	coord
	)

Definition at line 344 of file utils/tools/geodesy/functions.cpp.

operator<<() [8/12]

std::ostream& genesis::utils::operator<< ( std::ostream &  os, NexusBlock const &  block  )

inline

Definition at line 80 of file block.hpp.

operator<<() [9/12]

std::ostream & operator<<	(	std::ostream &	s,
		Bitvector const &	bv
	)

Insertion operator that outputs a Bitvector as a string of '0's and '1's.

Definition at line 161 of file utils/math/bitvector/operators.cpp.

operator<<() [10/12]

std::ostream & operator<<	(	std::ostream &	out,
		Style const &	style
	)

Print the properties of a Style object to a stream.

The application of Styles is usually done by invoking its operator(). However, in order to be able to show its properties at a glance, this operator instead prints them:

Style s( "blue" );
std::cout << s;

will print this information instead of a stylized text.

Definition at line 380 of file style.cpp.

operator<<() [11/12]

std::ostream & operator<<	(	std::ostream &	out,
		Table const &	table
	)

Definition at line 255 of file utils/text/table.cpp.

operator<<() [12/12]

std::ostream& genesis::utils::operator<<	(	std::ostream &	out,
		TableLayout::Binder const &	binder
	)

Definition at line 405 of file utils/text/table.cpp.

operator<=() [1/6]

bool genesis::utils::operator<=	(	JsonDocument const &	lhs,
		JsonDocument const &	rhs
	)

operator<=() [2/6]

bool genesis::utils::operator<= ( nullopt_t  , Optional< T > const &    )

inline

Definition at line 456 of file optional.hpp.

operator<=() [3/6]

bool genesis::utils::operator<= ( Optional< T > const &  x, nullopt_t    )

inline

Definition at line 450 of file optional.hpp.

operator<=() [4/6]

bool genesis::utils::operator<= ( Optional< T > const &  x, Optional< U > const &  y  )

inline

Definition at line 398 of file optional.hpp.

operator<=() [5/6]

bool genesis::utils::operator<= ( Optional< T > const &  x, U const &  v  )

inline

Definition at line 526 of file optional.hpp.

operator<=() [6/6]

bool genesis::utils::operator<= ( U const &  v, Optional< T > const &  x  )

inline

Definition at line 532 of file optional.hpp.

operator==() [1/11]

bool genesis::utils::operator== ( Color const &  lhs, Color const &  rhs  )

inline

Definition at line 212 of file color.hpp.

operator==() [2/11]

bool genesis::utils::operator==	(	JsonDocument const &	lhs,
		JsonDocument const &	rhs
	)

operator==() [3/11]

bool genesis::utils::operator==	(	JsonDocument const &	v,
		std::nullptr_t
	)

operator==() [4/11]

bool genesis::utils::operator==	(	JsonDocument::const_reference	lhs,
		JsonDocument::const_reference	rhs
	)

Compares two JSON values for equality according to the following rules:

• Two JSON values are equal if (1) they are from the same type and (2) their stored values are the same.
• Integer and floating-point numbers are automatically converted before comparison. Floating-point numbers are compared indirectly: two floating-point numbers f1 and f2 are considered equal if neither f1 > f2 nor f2 > f1 holds.
• Two JSON null values are equal. %

Definition at line 730 of file json/document.cpp.

operator==() [5/11]

bool genesis::utils::operator==	(	NexusTaxa const &	lhs,
		NexusTaxa const &	rhs
	)

Definition at line 100 of file taxa.hpp.

operator==() [6/11]

bool genesis::utils::operator== ( nullopt_t  , Optional< T > const &  x  )

inline

Definition at line 420 of file optional.hpp.

operator==() [7/11]

bool genesis::utils::operator== ( Optional< T > const &  x, nullopt_t    )

inline

Definition at line 414 of file optional.hpp.

operator==() [8/11]

bool genesis::utils::operator== ( Optional< T > const &  x, Optional< U > const &  y  )

inline

Definition at line 374 of file optional.hpp.

operator==() [9/11]

bool genesis::utils::operator== ( Optional< T > const &  x, U const &  v  )

inline

Definition at line 490 of file optional.hpp.

operator==() [10/11]

bool genesis::utils::operator==	(	std::nullptr_t	,
		JsonDocument const &	v
	)

operator==() [11/11]

bool genesis::utils::operator== ( U const &  v, Optional< T > const &  x  )

inline

Definition at line 496 of file optional.hpp.

operator>() [1/6]

bool genesis::utils::operator>	(	JsonDocument const &	lhs,
		JsonDocument const &	rhs
	)

operator>() [2/6]

bool genesis::utils::operator> ( nullopt_t  , Optional< T > const &    )

inline

Definition at line 468 of file optional.hpp.

operator>() [3/6]

bool genesis::utils::operator> ( Optional< T > const &  x, nullopt_t    )

inline

Definition at line 462 of file optional.hpp.

operator>() [4/6]

bool genesis::utils::operator> ( Optional< T > const &  x, Optional< U > const &  y  )

inline

Definition at line 392 of file optional.hpp.

operator>() [5/6]

bool genesis::utils::operator> ( Optional< T > const &  x, U const &  v  )

inline

Definition at line 538 of file optional.hpp.

operator>() [6/6]

bool genesis::utils::operator> ( U const &  v, Optional< T > const &  x  )

inline

Definition at line 544 of file optional.hpp.

operator>=() [1/6]

bool genesis::utils::operator>=	(	JsonDocument const &	lhs,
		JsonDocument const &	rhs
	)

operator>=() [2/6]

bool genesis::utils::operator>= ( nullopt_t  , Optional< T > const &  x  )

inline

Definition at line 480 of file optional.hpp.

operator>=() [3/6]

bool genesis::utils::operator>= ( Optional< T > const &  , nullopt_t    )

inline

Definition at line 474 of file optional.hpp.

operator>=() [4/6]

bool genesis::utils::operator>= ( Optional< T > const &  x, Optional< U > const &  y  )

inline

Definition at line 404 of file optional.hpp.

operator>=() [5/6]

bool genesis::utils::operator>= ( Optional< T > const &  x, U const &  v  )

inline

Definition at line 550 of file optional.hpp.

operator>=() [6/6]

bool genesis::utils::operator>= ( U const &  v, Optional< T > const &  x  )

inline

Definition at line 556 of file optional.hpp.

operator>>()

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'.

Definition at line 169 of file utils/math/bitvector/operators.cpp.

operator^()

Bitvector genesis::utils::operator^	(	Bitvector const &	lhs,
		Bitvector const &	rhs
	)

Definition at line 285 of file bitvector.cpp.

operator|()

Bitvector genesis::utils::operator|	(	Bitvector const &	lhs,
		Bitvector const &	rhs
	)

Definition at line 278 of file bitvector.cpp.

p_norm() [1/2]

double genesis::utils::p_norm	(	ForwardIterator	first,
		ForwardIterator	last,
		double	p = 2.0
	)

Calculate the p-norm 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 parameter p has to be >= 1.0. In order to get the maximum norm (or infinity norm), p can also be set to positive infinity, that is, std::numeric_limits<double>::infinity(). Default is p == 2.0, which is the Euclidean norm.

See also

euclidean_norm(), manhattan_norm(), and maximum_norm() for special cases, which simply call this function with a fixed p, in order to make code more expressive.

aitchison_norm() for another type of norm.

Definition at line 70 of file distance.hpp.

p_norm() [2/2]

double genesis::utils::p_norm ( std::vector< double > const &  vec, double  p = 2.0  )

inline

Calculate the p-norm of a std::vector of double elements.

See also

p_norm( ForwardIterator, ForwardIterator, double ) for details.

aitchison_norm() for another type of norm.

Definition at line 119 of file distance.hpp.

p_norm_distance() [1/2]

double genesis::utils::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.

The iterators first_a, last_a, first_b, and last_b need to point to a range of double values, with last_a and last_b being the past-the-end elements. The parameter p has to be >= 1.0. In order to get the maximum norm distance (or infinity norm distance), p can also be set to positive infinity, that is, std::numeric_limits<double>::infinity(). Default is p == 2.0, which is the Euclidean distance.

See https://en.wikipedia.org/wiki/Distance#Distance_in_Euclidean_space for details.

See also

euclidean_distance(), manhattan_distance(), and maximum_distance() for special cases, which simply call this function with a fixed p, in order to make code more expressive.

Definition at line 287 of file distance.hpp.

p_norm_distance() [2/2]

double genesis::utils::p_norm_distance ( std::vector< double > const &  vec_a, std::vector< double > const &  vec_b, double  p = 2.0  )

inline

Calculate the p-norm distance between two vectors of double elements.

See also

p_norm_distance( ForwardIteratorA, ForwardIteratorA, ForwardIteratorB, ForwardIteratorB, double ) for details.

Definition at line 339 of file distance.hpp.

p_norm_distance_matrix()

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.

The function uses p_norm_distance() to calculate the distances, see there for details. Each row of the matrix is considered a vector with the length of the columns of the matrix. Hence, the resulting quadratic distance matrix has dimensions r * r, with r being the number of rows of the input matrix.

See also

manhattan_distance_matrix(), euclidean_distance_matrix(), and maximum_distance_matrix() for specialized versions of this function with a fixed p for more expressive code.

Definition at line 48 of file distance.cpp.

parallel_block()

MultiFuture<R> genesis::utils::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.

The function takes a begin index and an end (past-the-end) index, and executes the body in num_blocks many blocks, by submitting tasks to the thread_pool, aiming to equally distribute the work across the range begin to end. In other words, it is equivalent to for( T i = begin; i < end; ++i ).

The body function to loop through is called once per block. It should take two arguments: the first index in the block and the index after the last index in the block, e.g.:

[]( size_t begin, size_t end ) {
    for( size_t i = begin; i < end; ++i ) {
        // ...
    }
}

The thread_pool defaults to using the Options::get().global_thread_pool(). This requires to call Options::get().init_global_thread_pool() first.

The num_blocks determines the number of blocks to split the loop body into. Default is to use the number of threads in the pool.

By default, auto_wait is set to true, meaning that the function blocks until the results are ready. This is meant as a convenience and safety mechanism, as otherwise the user might forget to wait, and continue with other things while the thread pool is still working on the blocks.

The function returns a MultiFuture that can be used to obtian the results for all the blocks. If auto_wait == false, this also can be used to call wait() on the returned MultiFuture to wait for all blocks to finish.

If the loop body returns a value, the MultiFuture can also be used to obtain the values returned by each block, for example:

[]( size_t begin, size_t end ) {
    size_t block_sum = 0;
    for( size_t i = begin; i < end; ++i ) {
        // ...
        block_sum += ...
    }
    return block_sum;
}

This is useful for example for aggregating values, such as a parallel sum.

Definition at line 143 of file thread_functions.hpp.

parallel_for()

MultiFuture<void> genesis::utils::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.

This is almost the same as parallel_block(), but intended to be used with for loops that do not need to compute per-block return values. The function signature of F is hence simply expected to be void F( size_t i ), and is called for every position in the processed range.

std::vector<int> numbers( 100 );
auto futures = pool->parallel_for(
    0, numbers.size(),
    [&numbers]( size_t i )
    {
        numbers[i] *= 2;
    }
);
futures.get();

This makes it a convenience function; see also parallel_for_each() for container-based data.

By default, auto_wait is set to true, meaning that the function first waits for all results to be ready, and only returns afterwards. Then, the returned future is ready immediately. This ensures that the user cannot accidentally forget to wait for the result, making this function behave more intuitively like an #pragma omp parallel for or the like.

Definition at line 259 of file thread_functions.hpp.

parallel_for_each() [1/2]

MultiFuture<void> genesis::utils::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.

Expects a random access container that supports size() as well as operator[] to access individual elements, and a body that takes one element of that container to process.

std::vector<int> numbers( 100 );
auto futures = pool->parallel_for_each(
    numbers,
    []( int& element )
    {
        element *= 2;
    }
);
futures.get();

This makes it a convenience function.

By default, auto_wait is set to true, meaning that the function first waits for all results to be ready, and only returns afterwards. Then, the returned future is ready immediately. This ensures that the user cannot accidentally forget to wait for the result, making this function behave more intuitively like an #pragma omp parallel for or the like.

Definition at line 369 of file thread_functions.hpp.

parallel_for_each() [2/2]

MultiFuture<void> genesis::utils::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.

This is almost the same as parallel_for(), but intended to be used with containers. The function signature of F is hence simply expected to be void F( T& element ) or void F( T const& element ), and is called for every element in the container.

std::vector<int> numbers( 100 );
auto futures = pool->parallel_for_each(
    numbers.begin(), numbers.end(),
    []( int& element )
    {
        element *= 2;
    }
);
futures.get();

This makes it a convenience function.

By default, auto_wait is set to true, meaning that the function first waits for all results to be ready, and only returns afterwards. Then, the returned future is ready immediately. This ensures that the user cannot accidentally forget to wait for the result, making this function behave more intuitively like an #pragma omp parallel for or the like.

Definition at line 306 of file thread_functions.hpp.

parse_float()

T genesis::utils::parse_float

(

utils::InputStream &

source

)

Read a floating point number from a stream and return it.

The number is expected to be in the following format:

[+-][123][.456][eE[+-]789]

It furthermore supports signed nan, inf, and infinity as special strings, case insensitive. The function stops reading at the first non-fitting character. It throws an std::overflow_error or underflow_error in case that the exponent (the part after the 'E') does not fit into integer value range.

Definition at line 176 of file parser.hpp.

parse_integer()

T genesis::utils::parse_integer

(

utils::InputStream &

source

)

Alias for parse_signed_integer().

Definition at line 154 of file parser.hpp.

parse_number_string()

std::string parse_number_string

(

utils::InputStream &

source

)

Read a general number string from an input stream.

The function reads from the input as long as it is a valid number of the format

[+-][123][.456][eE[+-]789]

and returns this string. This is useful for intermediately parsing a number and then checking whether it is valid. Use parse_float() to turn such a number string into an actual float/double.

Definition at line 479 of file parser.cpp.

parse_quoted_string()

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.

The first char of the stream is considered to be the opening quotation mark. Everything up until the closing quotation mark (the same char again, whatever it is) is then read. The stream is then pointing to the char right after the closing quotation mark.

If the string ends prematurely, i.e., without the closing quotation mark, or right after a backslash if use_escapes is used, the function throws an std::runtime_error.

Parameters

source	Stream to read from.
use_escapes	If this optional parameter is set to true, chars preceeded by a backslash \ are considered to be "escaped". If the char following the backslash is any of r, n or t, it is turned into its respective white space equivalent, while all other chars are copied verbatim to the return string. Thus, by escaping it, a the string can also include the quotation mark itself. Default of this parameter is true.
use_twin_quotes	If this optional parameter is set to true, the quotation mark itself can be escaped using two consecutive quotation marks. This works in addition to escaping it with a backslash (when use_escapes is used).
include_qmarks	The optional parameter include_qmarks demtermines whether the quotation marks are included in the output or not. Default is false.

Definition at line 547 of file parser.cpp.

parse_signed_integer()

T genesis::utils::parse_signed_integer

(

utils::InputStream &

source

)

Read a signed integer from a stream and return it.

The function expects a sequence of digits, possibly with a leading + or -. The first char after that has to be a digit, otherwise the function throws std::runtime_error. It stops reading at the first non-digit. In case the value range is too small, the function throws std::overflow_error, or underflow_error, respectively.

Definition at line 101 of file parser.hpp.

parse_unsigned_integer()

T genesis::utils::parse_unsigned_integer

(

utils::InputStream &

source

)

Read an unsigned integer from a stream and return it.

The function expects a sequence of digits. The current char in the stream has to be a digit, otherwise the function throws std::runtime_error. It stops reading at the first non-digit. In case the value range is too small, the function throws std::overflow_error.

Definition at line 68 of file parser.hpp.

parse_unsigned_integer_naive_()

size_t genesis::utils::parse_unsigned_integer_naive_

(

utils::InputStream &

source

)

Naive parsing that simply loops over chars.

Definition at line 401 of file parser.cpp.

parse_unsigned_integer_size_t()

size_t parse_unsigned_integer_size_t

(

utils::InputStream &

source

)

Parse the input source as an unsigned int into a size_t.

This is the basic parsing function that we use internally for the function templates parse_unsigned_integer() and parse_signed_integer(). That means, our internal int size cannot exceed 64 bits. That should be okay.

Definition at line 453 of file parser.cpp.

path_exists()

bool path_exists

(

std::string const &

path

)

Return whether a path exists, i.e., is a file or directory.

Definition at line 74 of file fs.cpp.

pcg32_rotr32()

static uint32_t genesis::utils::pcg32_rotr32 ( uint32_t  x, unsigned int  r  )

inlinestatic

Definition at line 53 of file random.cpp.

pearson_correlation_coefficient() [1/2]

double genesis::utils::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.

Both ranges need to have the same length. Then, the function calculates the PCC between the pairs of entries of both ranges. It skipes entries where any of the two values is not finite.

If each pair of entries in the ranges contains at leat one non-finite value, that is, if there are no pairs of finite values, a quiet_NaN is returned. Furtheremore, if one of the ranges has a standard deviation of 0.0, e.g., because all its entries are 0.0 themselves, a division by 0 occurs, leading to a NaN as well.

Definition at line 71 of file correlation.hpp.

pearson_correlation_coefficient() [2/2]

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

inline

Calculate the Pearson Correlation Coefficient between the entries of two vectors.

Both ranges need to have the same length. Then, the function calculates the PCC between the pairs of entries of both ranges. It skipes entries where any of the two values is not finite.

If each pair of entries in the ranges contains at leat one non-finite value, that is, if there are no pairs of finite values, a quiet_NaN is returned. Furtheremore, if one of the ranges has a standard deviation of 0.0, e.g., because all its entries are 0.0 themselves, a division by 0 occurs, leading to a NaN as well.

Definition at line 123 of file correlation.hpp.

permuted_congruential_generator() [1/3]

uint32_t permuted_congruential_generator

(

)

Fast random number generator for 32bit integers.

See https://en.wikipedia.org/wiki/Permuted_congruential_generator for details. See permuted_congruential_generator_init() to set the seed.

Definition at line 58 of file random.cpp.

permuted_congruential_generator() [2/3]

uint32_t permuted_congruential_generator

(

uint32_t

max

)

Fast random number generator for 32bit integers, for numbers in the range [0, max].

Note that the interval is closed, i.e., max is inclusive.

Definition at line 68 of file random.cpp.

permuted_congruential_generator() [3/3]

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].

Note that the interval is closed, i.e., max is inclusive.

Definition at line 73 of file random.cpp.

permuted_congruential_generator_bool() [1/2]

bool permuted_congruential_generator_bool

(

)

Fast random number generator for 32bit integers, for bool with 0.5 probability.

Definition at line 84 of file random.cpp.

permuted_congruential_generator_bool() [2/2]

bool permuted_congruential_generator_bool

(

uint32_t

chance_one_in

)

Fast random number generator for 32bit integers, for bool with a given chance.

This is returning a random bool, with a 1 in chance_one_in possibility to be true. For instance, calling the function with chance_one_in == 5 means a 1 in 5 chance, or probability of 0.2 for a true result.

Definition at line 89 of file random.cpp.

permuted_congruential_generator_init()

void permuted_congruential_generator_init

(

uint64_t

seed

)

Set the seed for permuted_congruential_generator().

Definition at line 99 of file random.cpp.

principal_component_analysis()

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.

Principal Components Analysis or the Karhunen-Loeve expansion is a classical method for dimensionality reduction or exploratory data analysis. One reference among many is: F. Murtagh and A. Heck, Multivariate Data Analysis, Kluwer Academic, Dordrecht, 1987.

Parameters

data	Matrix with the data, samples in rows, features in columns.
components	Intended number of PCA components to calculate. If 0 (default), all PCA components are calculated, i.e., as many components as data has columns.
standardization	Indicate the standardization algorithm to perfom on the data before calculating the PCA components, see PcaStandardization.

Returns

A struct that contains the eigenvalues and corresponding eigenvectors (i.e., the PCA components), and a Matrix with the projected data. See PcaData for details.

Definition at line 260 of file pca.cpp.

print() [1/2]

std::string genesis::utils::print	(	Matrix< T > const &	matrix,
		size_t	rows = 10,
		size_t	cols = 10
	)

Print a Matrix to a std::string.

If rows == 0, all rows are printed. Otherwise, only the given number of rows is printed, followed by an ellipsis (...). The same applies to the columns, using cols.

See also print( std::ostream&, Matrix<T> const&, size_t, size_t ).

Definition at line 285 of file utils/containers/matrix/operators.hpp.

print() [2/2]

void genesis::utils::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.

Definition at line 242 of file utils/containers/matrix/operators.hpp.

print_byte_matrix_()

void genesis::utils::print_byte_matrix_	(	std::ostream &	os,
		const Matrix< T > &	matrix,
		size_t	width
	)

Local helper function to avoid code duplication.

Definition at line 75 of file utils/containers/matrix/operators.cpp.

quartile_coefficient_of_dispersion() [1/2]

double genesis::utils::quartile_coefficient_of_dispersion ( Quartiles const &  q )

inline

Calculate the quartile_coefficient_of_dispersion.

The quartile coefficient of dispersion is defined as ( Q3 - Q1 ) / ( Q3 + Q1 ). See quartiles() to caculate those values. See https://en.wikipedia.org/wiki/Quartile_coefficient_of_dispersion for details.

Definition at line 1175 of file statistics.hpp.

quartile_coefficient_of_dispersion() [2/2]

std::vector<double> genesis::utils::quartile_coefficient_of_dispersion ( std::vector< Quartiles > const &  q )

inline

Calculate the quartile_coefficient_of_dispersion.

The quartile coefficient of dispersion is defined as ( Q3 - Q1 ) / ( Q3 + Q1 ). See quartiles() to caculate those values. See https://en.wikipedia.org/wiki/Quartile_coefficient_of_dispersion for details.

Definition at line 1183 of file statistics.hpp.

quartiles() [1/2]

Quartiles genesis::utils::quartiles	(	RandomAccessIterator	first,
		RandomAccessIterator	last
	)

Calculate the Quartiles of a sorted range of double values.

The iterators are as usual: first points to the first element of the range, last to the past-the-end element.

Definition at line 1066 of file statistics.hpp.

quartiles() [2/2]

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

inline

Calculate the Quartiles of a vector of double.

The vector has to be sorted.

Definition at line 1108 of file statistics.hpp.

ranking_dense() [1/2]

std::vector<size_t> genesis::utils::ranking_dense	(	RandomAccessIterator	first,
		RandomAccessIterator	last
	)

Return the ranking of the values in the given range, using Dense ranking ("1223" ranking).

See https://en.wikipedia.org/wiki/Ranking for details.

See also

ranking_standard(), ranking_modified(), ranking_ordinal(), ranking_fractional() for other ranking methods.

Definition at line 169 of file ranking.hpp.

ranking_dense() [2/2]

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

inline

Return the ranking of the values in the given range, using Dense ranking ("1223" ranking).

See https://en.wikipedia.org/wiki/Ranking for details.

See also

ranking_standard(), ranking_modified(), ranking_ordinal(), ranking_fractional() for other ranking methods.

Definition at line 201 of file ranking.hpp.

ranking_fractional() [1/2]

std::vector<double> genesis::utils::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).

See https://en.wikipedia.org/wiki/Ranking for details. This is the only raking method that returns float values instead of integer values.

See also

ranking_standard(), ranking_modified(), ranking_dense(), ranking_ordinal() for other ranking methods.

Definition at line 262 of file ranking.hpp.

ranking_fractional() [2/2]

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

inline

Return the ranking of the values in the given range, using Fractional ranking ("1 2.5 2.5 4" ranking).

See https://en.wikipedia.org/wiki/Ranking for details. This is the only raking method that returns float values instead of integer values.

See also

ranking_standard(), ranking_modified(), ranking_dense(), ranking_ordinal() for other ranking methods.

Definition at line 321 of file ranking.hpp.

ranking_modified() [1/2]

std::vector<size_t> genesis::utils::ranking_modified	(	RandomAccessIterator	first,
		RandomAccessIterator	last
	)

Return the ranking of the values in the given range, using Modified competition ranking ("1334" ranking).

See https://en.wikipedia.org/wiki/Ranking for details.

See also

ranking_standard(), ranking_dense(), ranking_ordinal(), ranking_fractional() for other ranking methods.

Definition at line 112 of file ranking.hpp.

ranking_modified() [2/2]

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

inline

Return the ranking of the values in the given range, using Modified competition ranking ("1334" ranking).

See https://en.wikipedia.org/wiki/Ranking for details.

See also

ranking_standard(), ranking_dense(), ranking_ordinal(), ranking_fractional() for other ranking methods.

Definition at line 151 of file ranking.hpp.

ranking_ordinal() [1/2]

std::vector<size_t> genesis::utils::ranking_ordinal	(	RandomAccessIterator	first,
		RandomAccessIterator	last
	)

Return the ranking of the values in the given range, using Ordinal ranking ("1234" ranking).

See https://en.wikipedia.org/wiki/Ranking for details.

See also

ranking_standard(), ranking_modified(), ranking_dense(), ranking_fractional() for other ranking methods.

Definition at line 219 of file ranking.hpp.

ranking_ordinal() [2/2]

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

inline

Return the ranking of the values in the given range, using Ordinal ranking ("1234" ranking).

See https://en.wikipedia.org/wiki/Ranking for details.

See also

ranking_standard(), ranking_modified(), ranking_dense(), ranking_fractional() for other ranking methods.

Definition at line 242 of file ranking.hpp.

ranking_standard() [1/2]

std::vector<size_t> genesis::utils::ranking_standard	(	RandomAccessIterator	first,
		RandomAccessIterator	last
	)

Return the ranking of the values in the given range, using Standard competition ranking ("1224" ranking).

See https://en.wikipedia.org/wiki/Ranking for details.

See also

ranking_modified(), ranking_dense(), ranking_ordinal(), ranking_fractional() for other ranking methods.

Definition at line 61 of file ranking.hpp.

ranking_standard() [2/2]

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

inline

Return the ranking of the values in the given range, using Standard competition ranking ("1224" ranking).

See https://en.wikipedia.org/wiki/Ranking for details.

See also

ranking_modified(), ranking_dense(), ranking_ordinal(), ranking_fractional() for other ranking methods.

Definition at line 93 of file ranking.hpp.

read_char_or_throw() [1/2]

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

inline

Lexing function that reads a single char from the stream and checks whether it equals the provided one.

If not, the function throws std::runtime_error. The stream is advanced by one position and the char is returned. For a similar function that checks the value of the current char but does not advance in the stream, see affirm_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 299 of file scanner.hpp.

read_char_or_throw() [2/2]

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

inline

Lexing function that reads a single char from the stream and checks whether it fulfills the provided criterion.

If not, the function throws std::runtime_error. The stream is advanced by one position and the char is returned. For a similar function that checks the value of the current char but does not advance in the stream, see affirm_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 340 of file scanner.hpp.

read_id_from_file_()

size_t genesis::utils::read_id_from_file_

(

std::string const &

filename

)

Definition at line 959 of file info.cpp.

read_to_end_of_line()

std::string genesis::utils::read_to_end_of_line ( InputStream &  source )

inline

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).

The stream is left at the new line char. If the stream is already at its last line, this function reads to the end of the stream.

Definition at line 134 of file scanner.hpp.

read_until() [1/2]

std::string genesis::utils::read_until ( InputStream &  source, char  criterion  )

inline

Lexing function that reads from the stream until its current char equals the provided one. The read chars are returned.

Definition at line 254 of file scanner.hpp.

read_until() [2/2]

std::string genesis::utils::read_until ( InputStream &  source, std::function< bool(char)>  criterion  )

inline

Lexing function that reads from the stream until its current char fulfills the provided criterion. The read chars are returned.

Definition at line 271 of file scanner.hpp.

read_while() [1/2]

std::string genesis::utils::read_while ( InputStream &  source, char  criterion  )

inline

Lexing function that reads from the stream while its current char equals the provided one. The read chars are returned.

Definition at line 216 of file scanner.hpp.

read_while() [2/2]

std::string genesis::utils::read_while ( InputStream &  source, std::function< bool(char)>  criterion  )

inline

Lexing function that reads from the stream while its current char fulfills the provided criterion. The read chars are returned.

Definition at line 233 of file scanner.hpp.

readlink_internal_()

static bool genesis::utils::readlink_internal_ ( const std::string &  path, std::string &  buffer, ssize_t  length  )

static

Definition at line 584 of file fs.cpp.

real_path()

std::string real_path	(	std::string const &	path,
		bool	resolve_link = true
	)

Return the real path of a file or directory, similar to realpath().

The function behaves similar to realpath(), but (hopefully) offers better protability and error handling (long paths etc).

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

Definition at line 731 of file fs.cpp.

real_path_realpath_()

static std::string genesis::utils::real_path_realpath_ ( std::string const &  path, bool  resolve_link  )

static

Definition at line 712 of file fs.cpp.

real_path_unix_()

static std::string genesis::utils::real_path_unix_ ( std::string const &  path, bool  resolve_link  )

static

Definition at line 672 of file fs.cpp.

realpath_file_()

static std::string genesis::utils::realpath_file_ ( const std::string &  path )

static

Definition at line 573 of file fs.cpp.

reduce_to_tridiagonal_matrix()

TridiagonalDecompositionData reduce_to_tridiagonal_matrix

(

Matrix< double > &

data

)

Triangular decomposition of a symmetric matrix.

This function performs an intermediate step that is usually followed by an execution of the tridiagonal_ql_algorithm().

It uses the Householder reduction of matrix a to tridiagonal form, according to

Martin et al., Num. Math. 11, 181-195, 1968.
Ref: Smith et al., Matrix Eigensystem Routines -- EISPACK Guide
Springer-Verlag, 1976, pp. 489-494.
W H Press et al., Numerical Recipes in C, Cambridge U P, 1988, pp. 373-374.

There, the function is called tred2().

The implementation of this function is largely borrowed from http://www.classification-society.org/csna/mda-sw/pca.c and http://ftp.uni-bayreuth.de/math/statlib/multi/pca.c published as Public Domain by Fionn Murtagh.

Parameters

data	Input data matrix. Operations are performed inline, that is, the matrix is changed during execution of the function.

Definition at line 49 of file pca.cpp.

relative_dir_base_split_()

static void genesis::utils::relative_dir_base_split_ ( std::string const &  path, std::string &  dir, std::string &  base  )

static

Definition at line 520 of file fs.cpp.

remove_all()

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.

Definition at line 761 of file string.cpp.

remove_all_chars()

std::string remove_all_chars	(	std::string const &	text,
		std::string const &	search_chars
	)

Remove all occurrences of the search_chars in text.

Definition at line 782 of file string.cpp.

remove_all_chars_pred()

std::string genesis::utils::remove_all_chars_pred	(	std::string const &	text,
		UnaryPredicate	predicate
	)

Remove all occurrences characters for which predicate is true in text.

Definition at line 430 of file string.hpp.

remove_all_non_alnum()

std::string remove_all_non_alnum

(

std::string const &

text

)

Remove all non-alphanumerical characters from a string.

Definition at line 794 of file string.cpp.

repeat()

std::string repeat	(	std::string const &	word,
		size_t	times
	)

Take a string and repeat it a given number of times.

Definition at line 1001 of file string.cpp.

replace_all()

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.

Definition at line 727 of file string.cpp.

replace_all_chars()

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.

Definition at line 768 of file string.cpp.

replace_all_chars_pred()

std::string genesis::utils::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.

Definition at line 404 of file string.hpp.

resolve_color_string()

Color resolve_color_string

(

std::string const &

color_str

)

Resolve a string representing a color.

The string can either be a hex color as accepted by color_from_hex(), e.g., "#003366[ff]", or one of the named colors, see is_color_name() and color_from_name().

Definition at line 138 of file utils/color/functions.cpp.

round_to()

double genesis::utils::round_to ( double  x, size_t  accuracy_order  )

inline

Retun the value of x, rounded to the decimal digit given by accuracy_order.

Definition at line 175 of file common.hpp.

sanitize_filename()

std::string sanitize_filename

(

std::string const &

filename

)

Remove or replace all invalid parts of a filename.

Similar to is_valid_filename(), this function is not meant to be an ultimate solution to valid filenames. See there for details.

The function is meant to be called on the file name itself, without the directory path leading to it. File extensions are allowed. Thus, you might need to call file_basename() before in order to get the file name without the path.

This function does the following:

• All non-printable characters are removed.
• Spaces at the beginning and end are removed.
• All invalid chars are replaced by an underscore. See is_valid_filename() for a list of those chars.

If after this procedure the filename is empty, an exception is thrown. This is meant to save the user from checking this, or from running into trouble when trying to write to this "file" - because an empty filename will point to a directory name.

Definition at line 863 of file fs.cpp.

sanitize_geo_coordinate()

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.

The function replaces symbols such as degrees, primes, double primes by simple letters ('dms') that serve the same function.

Furthermore, if two_components is true (default), the function assumes that the given coordinate contains two components (North/South and East/West). In that case, if there is exaclty one comma in the input, it is replaced by a slash. This is meant to avoid ambiguity in parsing of a coordinate that uses commas as decimal separator. Hence, when sanitizing a coordinate with only one component, two_components needs to be set to false in order to avoid replacing a single decimal separator comma by a slash.

Definition at line 198 of file utils/tools/geodesy/functions.cpp.

scale()

void scale	(	Histogram &	h,
		double	factor
	)

Definition at line 54 of file operations.cpp.

select_without_replacement()

std::vector< size_t > select_without_replacement	(	size_t	k,
		size_t	n
	)

Select k many unique numbers out of the range [ 0, n ).

In other words, select k numbers out of the sequence of n numbers, without replacement.

The implementation is based on Algorithm 3.4.2S of Knuth's book Seminumeric Algorithms.

Parameters

k	Desired sample size.
n	Total population size.

Returns

List of k unique numbers out of the range [ 0, n ).

Definition at line 108 of file random.cpp.

set_minus()

Bitvector set_minus	(	Bitvector const &	lhs,
		Bitvector const &	rhs
	)

Definition at line 84 of file utils/math/bitvector/operators.cpp.

sigma()

double sigma

(

const Histogram &

h

)

Compute the bin-weighted standard deviation.

The histogram is regarded as a probability distribution. Negative bin values are ignored for the purposes of this calculation. The accuracy of the result is limited by the bin width.

Definition at line 114 of file utils/math/histogram/stats.cpp.

signum() [1/3]

constexpr int genesis::utils::signum ( T  x )

inlineconstexpr

Get the sign of a value, which is either -1, 0, or 1.

Works for all numerical types. We use two tagged implementations for signed and unsigned types in order to avoid compiler warnings. See http://stackoverflow.com/questions/1903954/is-there-a-standard-sign-function-signum-sgn-in-c-c for details.

Definition at line 133 of file common.hpp.

signum() [2/3]

constexpr int genesis::utils::signum ( T  x, std::false_type    )

inlineconstexpr

Implementation of signum(T x) for unsigned types. See there for details.

Definition at line 104 of file common.hpp.

signum() [3/3]

constexpr int genesis::utils::signum ( T  x, std::true_type    )

inlineconstexpr

Implementation of signum(T x) for signed types. See there for details.

Definition at line 116 of file common.hpp.

simple_frame()

TableLayout simple_frame

(

bool

condensed

)

Definition at line 483 of file utils/text/table.cpp.

simple_grid()

TableLayout simple_grid

(

bool

condensed

)

Definition at line 464 of file utils/text/table.cpp.

simple_layout()

TableLayout simple_layout

(

bool

condensed

)

Definition at line 445 of file utils/text/table.cpp.

simple_linear_regression()

LinearFunction genesis::utils::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.

See https://en.wikipedia.org/wiki/Simple_linear_regression for an explanation.

See also

mean_squared_error() for calculating the resulting error.

Definition at line 74 of file slr.hpp.

skip_to_end_of_line()

void genesis::utils::skip_to_end_of_line ( InputStream &  source )

inline

Lexing function that advances the stream to the end of the line, i.e., to the new line char.

If the stream is already at its last line, this function moves to the end of the stream.

Definition at line 118 of file scanner.hpp.

skip_until() [1/2]

void genesis::utils::skip_until ( InputStream &  source, char  criterion  )

inline

Lexing function that advances the stream until its current char equals the provided one.

Definition at line 184 of file scanner.hpp.

skip_until() [2/2]

void genesis::utils::skip_until ( InputStream &  source, std::function< bool(char)>  criterion  )

inline

Lexing function that advances the stream until its current char fulfills the provided criterion.

Definition at line 198 of file scanner.hpp.

skip_while() [1/2]

void genesis::utils::skip_while ( InputStream &  source, char  criterion  )

inline

Lexing function that advances the stream while its current char equals the provided one.

Definition at line 153 of file scanner.hpp.

skip_while() [2/2]

void genesis::utils::skip_while ( InputStream &  source, std::function< bool(char)>  criterion  )

inline

Lexing function that advances the stream while its current char fulfills the provided criterion.

Definition at line 167 of file scanner.hpp.

sort_indices() [1/2]

std::vector<size_t> genesis::utils::sort_indices ( RandomAccessIterator  first, RandomAccessIterator  last  )

inline

Get the indices to the sorted order of the given range.

This function returns a list of indices into the given range, so that their order gives the sorted content of the elements in [ first, last ), using std::less for comparisons.

For example,

for( auto i: sort_indices(v) ) {
    cout << *( first + i ) << endl;
}

outputs the elements in the range in sorted order, without actually moving any elements in the range. This is useful if the same sorting order needs to be applied to some other container.

There is also an overload of this function that takes an additional parameter comparator. It can be used to specify the function for comparing two values of the range.

Furthermore, there are variants that use std::stable_sort instead, see stable_sort_indices().

Definition at line 224 of file algorithm.hpp.

sort_indices() [2/2]

std::vector<size_t> genesis::utils::sort_indices ( RandomAccessIterator  first, RandomAccessIterator  last, Comparator  comparator  )

inline

Get the indices to the sorted order of the given range.

This function returns a list of indices into the given range, so that their order gives the sorted content of the elements in [ first, last ), using std::less for comparisons.

For example,

for( auto i: sort_indices(v) ) {
    cout << *( first + i ) << endl;
}

outputs the elements in the range in sorted order, without actually moving any elements in the range. This is useful if the same sorting order needs to be applied to some other container.

There is also an overload of this function that takes an additional parameter comparator. It can be used to specify the function for comparing two values of the range.

Furthermore, there are variants that use std::stable_sort instead, see stable_sort_indices().

Definition at line 182 of file algorithm.hpp.

sort_natural()

void genesis::utils::sort_natural ( RandomAccessIterator  first, RandomAccessIterator  last, bool  reverse = false  )

inline

Sort a range of std::string (or convertible to std::string) elements, using natural sorting; see compare_natural().

Definition at line 246 of file string.hpp.

spearmans_rank_correlation_coefficient() [1/2]

double genesis::utils::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.

Both ranges need to have the same length. Then, the function calculates Spearmans's Rho between the pairs of entries of both vectors. Ranking is done via fractional ranking. Pairs of entries which contain non-finite values are skipped.

Definition at line 145 of file correlation.hpp.

spearmans_rank_correlation_coefficient() [2/2]

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

inline

Calculate Spearman's Rank Correlation Coefficient between the entries of two vectors.

Both ranges need to have the same length. Then, the function calculates Spearmans's Rho between the pairs of entries of both vectors. Ranking is done via fractional ranking. Pairs of entries which contain non-finite values are skipped.

Definition at line 166 of file correlation.hpp.

split() [1/3]

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.

The string is split using the delimiter char, and returned as a vector of strings. If trim_empty is set, empty strings resulting from adjacent delimiter chars are excluded from the output.

Definition at line 575 of file string.cpp.

split() [2/3]

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.

The string is split using any of the chars for which delimiter_predicate is true, and returned as a vector of strings. If trim_empty is set, empty strings resulting from adjacent delimiter chars are excluded from the output.

Definition at line 598 of file string.cpp.

split() [3/3]

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.

The string is split using any of the chars in delimiters, and returned as a vector of strings. If trim_empty is set, empty strings resulting from adjacent delimiter chars are excluded from the output.

Definition at line 583 of file string.cpp.

split_()

static std::vector<std::string> genesis::utils::split_ ( std::string const &  string, std::function< size_t(std::string const &, size_t)>  find_pos, size_t  advance_by, const bool  trim_empty  )

static

Local function that does the work for the split cuntions.

Definition at line 539 of file string.cpp.

split_at()

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.

The string is split where the whole delimiter string is found, and returned as a vector of strings. If trim_empty is set, empty strings resulting from adjacent delimiters are excluded from the output.

Definition at line 621 of file string.cpp.

split_range_list()

std::vector< size_t > split_range_list

(

std::string const &

str

)

Split a string containing positive interger numbers into its parts and resolve ranges.

For example, the string 1, 3, 5-7, 10 results in a vector of all listed numbers and the ranges in between, that is 1, 3, 5, 6, 7, 10. Whitespace is ignored; the range is sorted.

Definition at line 636 of file string.cpp.

squared()

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

inlineconstexpr

Square of a number.

Simply \( x^2 \), but faster than std::pow for the low exponent. Meant as an abbreviation where the argument is not already a variable, e.g., squared( x - 1.0 ), without the need to store the intermediate argument term.

Definition at line 223 of file common.hpp.

stable_sort_indices() [1/2]

std::vector<size_t> genesis::utils::stable_sort_indices ( RandomAccessIterator  first, RandomAccessIterator  last  )

inline

Get the indices to the stable sorted order of the given range.

This function returns a list of indices into the given range, so that their order gives the stable sorted content of the elements in [ first, last ), using std::less for comparisons.

For example,

for( auto i: stable_sort_indices(v) ) {
    cout << *( first + i ) << endl;
}

outputs the elements in the range in stable sorted order, without actually moving any elements in the range. This is useful if the same sorting order needs to be applied to some other container.

There is also an overload of this function that takes an additional parameter comparator. It can be used to specify the function for comparing two values of the range.

Furthermore, there are variants that use normal std::sort instead, see sort_indices().

Definition at line 281 of file algorithm.hpp.

stable_sort_indices() [2/2]

std::vector<size_t> genesis::utils::stable_sort_indices ( RandomAccessIterator  first, RandomAccessIterator  last, Comparator  comparator  )

inline

Get the indices to the stable sorted order of the given range.

This function returns a list of indices into the given range, so that their order gives the stable sorted content of the elements in [ first, last ), using std::less for comparisons.

For example,

for( auto i: stable_sort_indices(v) ) {
    cout << *( first + i ) << endl;
}

outputs the elements in the range in stable sorted order, without actually moving any elements in the range. This is useful if the same sorting order needs to be applied to some other container.

There is also an overload of this function that takes an additional parameter comparator. It can be used to specify the function for comparing two values of the range.

Furthermore, there are variants that use normal std::sort instead, see sort_indices().

Definition at line 239 of file algorithm.hpp.

standardize_cols()

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.

The function performs a column-wise z-transformation on the given data.

The function returns a vector containing the mean and standard deviation of the columns before standardization, see MeanStddevPair. If both scale_means and scale_std are set to false, the original data is not manipulated, while the returned vector still contains the means and standard deviations. See also matrix_col_mean_stddev().

Parameters

data	Input data Matrix; standardizing is done inline.
scale_means	If true (default), center the data by subtracting the mean per column.
scale_std	If true (default), scale the data to unit variance (or equivalently, unit standard deviation) per column.

Returns

Vector containing the mean and standard deviation for each column before standardization.

Definition at line 94 of file math/matrix.cpp.

standardize_rows()

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.

The function performs a row-wise z-transformation on the given data.

The function returns a vector containing the mean and standard deviation of the rows before standardization, see MeanStddevPair. If both scale_means and scale_std are set to false, the original data is not manipulated, while the returned vector still contains the means and standard deviations. See also matrix_row_mean_stddev().

Parameters

data	Input data Matrix; standardizing is done inline.
scale_means	If true (default), center the data by subtracting the mean per column.
scale_std	If true (default), scale the data to unit variance (or equivalently, unit standard deviation) per column.

Returns

Vector containing the mean and standard deviation for each column before standardization.

Definition at line 124 of file math/matrix.cpp.

starts_with() [1/2]

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.

Definition at line 136 of file string.cpp.

starts_with() [2/2]

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.

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

Definition at line 144 of file string.cpp.

starts_with_ci() [1/2]

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.

Definition at line 154 of file string.cpp.

starts_with_ci() [2/2]

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.

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

Definition at line 160 of file string.cpp.

starts_with_ci_alnum() [1/2]

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.

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

Definition at line 170 of file string.cpp.

starts_with_ci_alnum() [2/2]

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.

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

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

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

Definition at line 177 of file string.cpp.

strcasecmp()

int strcasecmp	(	char const *	s1,
		char const *	s2
	)

Compares two strings, ignoring case differences.

Compares the null-terminated strings s1 and s2, returning -1, 0, or 1 if s1 is lexicographically less than, equal to, or greater than s2 over those characters, respectively.

This is equivalent to the POSIX function of the same name, found in strings.h, but included here for portability.

Definition at line 84 of file string.cpp.

strerror_()

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

static

Overload of error-reporting function, to enable use with VS.

Ref: http://stackoverflow.com/a/901316/717706

Definition at line 87 of file strict_fstream.cpp.

strncasecmp()

int strncasecmp	(	char const *	s1,
		char const *	s2,
		size_t	n
	)

Compares up to n chars of two strings, ignoring case differences.

Compares up to n chars of the null-terminated strings s1 and s2, returning -1, 0, or 1 if s1 is lexicographically less than, equal to, or greater than s2 over those characters, respectively.

This is equivalent to the POSIX function of the same name, found in strings.h, but included here for portability.

Definition at line 90 of file string.cpp.

sum()

double sum

(

const Histogram &

h

)

Definition at line 140 of file utils/math/histogram/stats.cpp.

summarize_column() [1/2]

std::string summarize_column	(	Dataframe const &	df,
		size_t	col_index
	)

Definition at line 266 of file utils/containers/dataframe/operators.cpp.

summarize_column() [2/2]

std::string summarize_column	(	Dataframe const &	df,
		std::string const &	col_name
	)

Definition at line 298 of file utils/containers/dataframe/operators.cpp.

summarize_column_common_()

std::string genesis::utils::summarize_column_common_	(	Dataframe const &	df,
		size_t	col_index,
		std::string const &	description
	)

Definition at line 216 of file utils/containers/dataframe/operators.cpp.

summarize_column_double_()

std::string genesis::utils::summarize_column_double_	(	Dataframe const &	df,
		size_t	col_index
	)

Definition at line 222 of file utils/containers/dataframe/operators.cpp.

summarize_column_int_()

std::string genesis::utils::summarize_column_int_	(	Dataframe const &	df,
		size_t	col_index
	)

Definition at line 243 of file utils/containers/dataframe/operators.cpp.

summarize_column_string_()

std::string genesis::utils::summarize_column_string_	(	Dataframe const &	df,
		size_t	col_index
	)

Definition at line 254 of file utils/containers/dataframe/operators.cpp.

summarize_columns()

std::string summarize_columns

(

Dataframe const &

df

)

Definition at line 304 of file utils/containers/dataframe/operators.cpp.

sums_of_squares_and_cross_products_matrix()

Matrix< double > sums_of_squares_and_cross_products_matrix

(

Matrix< double > const &

data

)

Calculate the Sums of Squares and Cross Products Matrix (SSCP Matrix).

Definition at line 225 of file math/matrix.cpp.

svg_arc()

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.

Example:

SvgPath(
    { svg_arc( 0, 0, 10, start_a, end_a ) },
    stroke
);

The angles are measured in radians, and always drawn clockwise from start to end. If wedge is given, the path is drawn including segments to the circle center; otherwise, the path position is moved to the beginning of the arc first, and left at its end.

Definition at line 50 of file utils/formats/svg/helper.cpp.

svg_attribute()

std::string genesis::utils::svg_attribute	(	std::string const &	name,
		T const &	value,
		std::string const &	unit = ""
	)

Definition at line 229 of file utils/formats/svg/helper.hpp.

svg_bounding_box() [1/2]

SvgBox svg_bounding_box

(

std::vector< SvgPoint > const &

points

)

Compute the bounding box of a set of points.

Definition at line 87 of file utils/formats/svg/helper.cpp.

svg_bounding_box() [2/2]

SvgBox svg_bounding_box	(	std::vector< SvgPoint > const &	points,
		SvgTransform const &	transform
	)

Compute the bounding box of a set of points, including their transformation.

Definition at line 112 of file utils/formats/svg/helper.cpp.

svg_comment()

std::string genesis::utils::svg_comment ( std::string const &  content )

inline

Definition at line 223 of file utils/formats/svg/helper.hpp.

svg_data_uri()

std::string genesis::utils::svg_data_uri ( std::string const &  media_type, std::string const &  content, bool  encode_base64 = false  )

inline

Definition at line 239 of file utils/formats/svg/helper.hpp.

swap() [1/12]

void genesis::utils::swap ( BlockingConcurrentQueue< T, Traits > &  a, BlockingConcurrentQueue< T, Traits > &  b  )

inline

Definition at line 629 of file blocking_concurrent_queue.hpp.

swap() [2/12]

void genesis::utils::swap ( Color &  lhs, Color &  rhs  )

inline

Definition at line 207 of file color.hpp.

swap() [3/12]

void genesis::utils::swap ( ConcurrentQueue< T, Traits > &  a, ConcurrentQueue< T, Traits > &  b  )

inlinenoexcept

Definition at line 3914 of file concurrent_queue.hpp.

swap() [4/12]

void genesis::utils::swap ( ConsumerToken &  a, ConsumerToken &  b  )

inlinenoexcept

Definition at line 3924 of file concurrent_queue.hpp.

swap() [5/12]

void swap	(	Histogram &	lhs,
		Histogram &	rhs
	)

Definition at line 47 of file histogram.cpp.

swap() [6/12]

void genesis::utils::swap ( HistogramAccumulator &  lhs, HistogramAccumulator &  rhs  )

inline

Definition at line 154 of file accumulator.hpp.

swap() [7/12]

void genesis::utils::swap ( NexusTaxa &  lhs, NexusTaxa &  rhs  )

inline

Definition at line 209 of file taxa.hpp.

swap() [8/12]

void genesis::utils::swap ( NexusTrees &  lhs, NexusTrees &  rhs  )

inline

Definition at line 242 of file trees.hpp.

swap() [9/12]

void genesis::utils::swap	(	Optional< T > &	x,
		Optional< T > &	y
	)

Definition at line 566 of file optional.hpp.

swap() [10/12]

void genesis::utils::swap ( ProducerToken &  a, ProducerToken &  b  )

inlinenoexcept

Definition at line 3919 of file concurrent_queue.hpp.

swap() [11/12]

void genesis::utils::swap ( Style &  lhs, Style &  rhs  )

inline

Definition at line 198 of file style.hpp.

swap() [12/12]

void swap ( typename ConcurrentQueue< T, Traits >::ImplicitProducerKVP &  a, typename ConcurrentQueue< T, Traits >::ImplicitProducerKVP &  b  )

inlinenoexcept

Definition at line 3930 of file concurrent_queue.hpp.

swap_cols()

void genesis::utils::swap_cols	(	Matrix< T > &	data,
		size_t	col_a,
		size_t	col_b
	)

Swap (interchange) two columns of a Matrix, given their indices.

Definition at line 316 of file utils/containers/matrix/operators.hpp.

swap_rows()

void genesis::utils::swap_rows	(	Matrix< T > &	data,
		size_t	row_a,
		size_t	row_b
	)

Swap (interchange) two rows of a Matrix, given their indices.

Definition at line 300 of file utils/containers/matrix/operators.hpp.

symlink_resolve_()

static bool genesis::utils::symlink_resolve_ ( const std::string &  start, std::string &  end  )

static

Definition at line 621 of file fs.cpp.

symmetric_difference()

Bitvector symmetric_difference	(	Bitvector const &	lhs,
		Bitvector const &	rhs
	)

Definition at line 89 of file utils/math/bitvector/operators.cpp.

tail()

std::string tail	(	std::string const &	text,
		size_t	lines
	)

Return the last lines of the text.

Definition at line 505 of file string.cpp.

time_to_tm() [1/3]

std::vector<std::tm> genesis::utils::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.

By default, we use Coordinated Universal Time (UTC), so that results are reproducible. If local time is needed instead, set use_local_time to true.

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

Definition at line 123 of file date_time.hpp.

time_to_tm() [2/3]

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.

By default, we use Coordinated Universal Time (UTC), so that results are reproducible. If local time is needed instead, set use_local_time to true.

Definition at line 147 of file date_time.cpp.

time_to_tm() [3/3]

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.

By default, we use Coordinated Universal Time (UTC), so that results are reproducible. If local time is needed instead, set use_local_time to true.

Definition at line 170 of file date_time.cpp.

tm_date_to_string()

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.

The format is %Y-%m-%d, for example 2020-04-17.

Definition at line 213 of file date_time.cpp.

tm_time_to_string()

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.

The format is %H:%M:%S, for example 00:27:58.

Definition at line 218 of file date_time.cpp.

tm_to_string() [1/3]

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.

The format is %Y-%m-%dT%H:%M:%S, for example 2020-04-17T00:27:58.

Definition at line 208 of file date_time.cpp.

tm_to_string() [2/3]

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.

If the format uses locale-depended qualifiers, the "C" locale is used.

Definition at line 203 of file date_time.cpp.

tm_to_string() [3/3]

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.

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 179 of file date_time.cpp.

tm_to_time() [1/3]

std::vector<std::time_t> genesis::utils::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.

By default, we use Coordinated Universal Time (UTC), so that results are reproducible. If local time is needed instead, set use_local_time to true.

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

Definition at line 80 of file date_time.hpp.

tm_to_time() [2/3]

std::time_t tm_to_time	(	std::tm	time,
		bool	use_local_time = false
	)

Convert std::tm object to a std::time_t object.

By default, we use Coordinated Universal Time (UTC), so that results are reproducible. If local time is needed instead, set use_local_time to true.

Definition at line 108 of file date_time.cpp.

tm_to_time() [3/3]

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.

By default, we use Coordinated Universal Time (UTC), so that results are reproducible. If local time is needed instead, set use_local_time to true.

Definition at line 142 of file date_time.cpp.

to_bit_string()

std::string genesis::utils::to_bit_string ( T const  x, char const  zero = '0', char const  one = '1', bool const  byte_space = true  )

inline

Return the bit representation of an unsigned int.

For example, to_bit_string(5) yields "0...0101". Optionally, the chars to use for zero and one can be set, as well as a flag whether to put spaces in between individual bytes of the output.

Definition at line 659 of file string.hpp.

to_file() [1/2]

std::shared_ptr<BaseOutputTarget> genesis::utils::to_file ( std::string const &  file_name, GzipCompressionLevel  compression_level, bool  auto_adjust_filename = true  )

inline

Obtain an output target for writing to a file.

The output target returned from this function can be used in the writer classes, e.g., placement::JplaceWriter or sequence::FastaWriter.

If compression_level is set to a compression level other than GzipCompressionLevel::kNoCompression, the output is compressed using gzip. We recommend to use GzipCompressionLevel::kDefaultCompression%.

Furthermore, if auto_adjust_filename is set to true (default), the file name is adjusted according to the compression setting: If compression is used, the file name is appended by the .gz extension, if this is not alreay present. (For completeness, the oppositve also works: If the file name ends in .gz, but no compression is chosen, the .gz extension is removed.)

If the file cannot be written to, the function throws an exception. Also, by default, if the file already exists, an exception is thrown. See Options::allow_file_overwriting() to change this behaviour.

See also to_gzip_block_file() for a version that offers multithreaded gzip compression using blocks of compressed data.

Definition at line 81 of file output_target.hpp.

to_file() [2/2]

std::shared_ptr<BaseOutputTarget> genesis::utils::to_file ( std::string const &  file_name, std::ios_base::openmode  mode = std::ios_base::out  )

inline

Obtain an output target for writing to a file, using a specific output mode.

The output target returned from this function can be used in the writer classes, e.g., placement::JplaceWriter or sequence::FastaWriter.

This version of the function allows to explicitly set the openmode, which is for example useful to append to an existing file, or to open it in binary mode.

Definition at line 117 of file output_target.hpp.

to_gzip_block_file()

std::shared_ptr<BaseOutputTarget> genesis::utils::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  )

inline

Obtain an output target for writing gzip block compressed data to a file.

This output target uses multithreaded gzip compression by block-compressing chunks of data. See GzipBlockOStream for an explanation and more details on this technique and the parameters offered here.

For general details on using this output target for writing data, see to_file().

See also

GzipBlockOStream

GzipBlockOutputTarget

to_file()

Definition at line 151 of file output_target.hpp.

to_gzip_file()

std::shared_ptr<BaseOutputTarget> genesis::utils::to_gzip_file ( std::string const &  file_name )

inline

Obtain an output target for writing to a gzip-compressed file.

The output target returned from this function can be used in the writer classes, e.g., placement::JplaceWriter or sequence::FastaWriter.

See also

to_file(), this is a wrapper that automatically sets GzipCompressionLevel::kDefaultCompression

Definition at line 132 of file output_target.hpp.

to_lower() [1/2]

constexpr char genesis::utils::to_lower ( char  c )

constexprnoexcept

Return the lower case version of a letter, ASCII-only.

Definition at line 221 of file char.hpp.

to_lower() [2/2]

std::string genesis::utils::to_lower ( std::string const &  str )

inline

Return an all-lowercase copy of the given string, locale-aware.

Definition at line 478 of file string.hpp.

to_lower_ascii()

std::string to_lower_ascii

(

std::string const &

str

)

Return an all-lowercase copy of the given string, ASCII-only.

Definition at line 895 of file string.cpp.

to_lower_ascii_inplace()

void to_lower_ascii_inplace

(

std::string &

str

)

Turn the given string to all-lowercase, ASCII-only.

Definition at line 878 of file string.cpp.

to_lower_inplace()

void genesis::utils::to_lower_inplace ( std::string &  str )

inline

Turn the given string to all-lowercase, locale-aware.

Definition at line 492 of file string.hpp.

to_nucleic_acids()

std::string to_nucleic_acids

(

TwobitVector const &

vec

)

Turn a TwobitVector into its string representation of nucleic acids.

Definition at line 107 of file utils/math/twobit_vector/functions.cpp.

to_stderr()

std::shared_ptr<BaseOutputTarget> genesis::utils::to_stderr ( )

inline

Obtain an output target for writing to standard error (i.e., stderr or cerr).

The output target returned from this function can be used in the writer classes, e.g., placement::JplaceWriter or sequence::FastaWriter.

Definition at line 232 of file output_target.hpp.

to_stdout()

std::shared_ptr<BaseOutputTarget> genesis::utils::to_stdout ( )

inline

Obtain an output target for writing to standard output (i.e., stdout or cout).

The output target returned from this function can be used in the writer classes, e.g., placement::JplaceWriter or sequence::FastaWriter.

Definition at line 222 of file output_target.hpp.

to_stream()

std::shared_ptr<BaseOutputTarget> genesis::utils::to_stream ( std::ostream &  target_stream, GzipCompressionLevel  compression_level = GzipCompressionLevel::kNoCompression  )

inline

Obtain an output target for writing to a stream.

The output target returned from this function can be used in the writer classes, e.g., placement::JplaceWriter or sequence::FastaWriter.

If compression_level is set to a compression level other than GzipCompressionLevel::kNoCompression (which is the default, which means, no compression by default), the output is compressed using gzip. In that case, it is recommended that the target_stream uses std::ios_base::binary when opening the stream.

Definition at line 203 of file output_target.hpp.

to_string()

std::shared_ptr<BaseOutputTarget> genesis::utils::to_string ( std::string &  target_string )

inline

Obtain an output target for writing to a string.

The output target returned from this function can be used in the writer classes, e.g., placement::JplaceWriter or sequence::FastaWriter.

Definition at line 186 of file output_target.hpp.

to_string_byte_format()

std::string to_string_byte_format

(

size_t

value

)

Produce a human readable formatting of a size in bytes, using the appropriate suffix.

For instance, this function produces 123MB.

Definition at line 1047 of file string.cpp.

to_string_leading_zeros()

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.

If value is already longer than length, the result will also be longer.

Definition at line 1014 of file string.cpp.

to_string_nice()

std::string genesis::utils::to_string_nice

(

T const &

v

)

Return a string representation of a given value.

This function template is a drop-in replacement for std::to_string, with the difference that it treats floating point numbers more nicely: Instead of printing a fixed amount of digits, it only prints digits without trailing zeros.

If you also want to round the value, or need more precision, see to_string_precise() and to_string_rounded().

As it uses operator << on the given value, it is suitable for any class or value for which this stream operator is available. Thus, this function can also be used for conveniently returning a string where otherwise some stream operations would have been necessary.

Definition at line 637 of file string.hpp.

to_string_precise()

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).

This function rounds the value to the given precision, and then returns its string representation with possible trailing zeros. Thus, it uses fixed precision. This is useful for e.g., output in a table format.

For a version of this function that truncates trailing zeros, see to_string_rounded(). Also, see to_string() if you simply want to output a string representation of a double.

Definition at line 1021 of file string.cpp.

to_string_rounded()

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.

This function rounds the value to the given precision, and then returns its string representation without trailing zeros. This is useful for output that keeps a certain amount of significant decimal digits, while making the output as short as possible.

If you want to round, but also keep trailing zeros, see to_string_precise(). Also, see to_string() if you simply want to output a string representation of a double.

Definition at line 1029 of file string.cpp.

to_upper() [1/2]

constexpr char genesis::utils::to_upper ( char  c )

constexprnoexcept

Return the upper case version of a letter, ASCII-only.

Definition at line 230 of file char.hpp.

to_upper() [2/2]

std::string genesis::utils::to_upper ( std::string const &  str )

inline

Return an all-uppercase copy of the given string, locale-aware.

Definition at line 502 of file string.hpp.

to_upper_ascii()

std::string to_upper_ascii

(

std::string const &

str

)

Return an all-uppercase copy of the given string, ASCII-only.

Definition at line 919 of file string.cpp.

to_upper_ascii_inplace()

void to_upper_ascii_inplace

(

std::string &

str

)

Turn the given string to all-uppercase, ASCII-only, inline.

Uses AVX2 if available.

Definition at line 902 of file string.cpp.

to_upper_inplace()

void genesis::utils::to_upper_inplace ( std::string &  str )

inline

Turn the given string to all-uppercase, locale-aware.

Definition at line 514 of file string.hpp.

translate_from_nucleic_acid()

TwobitVector::ValueType translate_from_nucleic_acid

(

char

site

)

Translate a char into TwobitVector::ValueType.

Valid chars are A, C, G, T, and their lower case variants.

Definition at line 49 of file utils/math/twobit_vector/functions.cpp.

translate_to_nucleic_acid()

char translate_to_nucleic_acid

(

TwobitVector::ValueType

value

)

Translate a TwobitVector::ValueType into its char representation.

This gives one of the values A, C, G and T.

Definition at line 78 of file utils/math/twobit_vector/functions.cpp.

transpose()

Matrix<T> genesis::utils::transpose

(

Matrix< T > const &

mat

)

Transpose a Matrix.

Definition at line 127 of file utils/containers/matrix/operators.hpp.

transpose_inplace()

void transpose_inplace

(

Matrix< T > &

mat

)

Transpose a Matrix inplace, without allocating a new Matrix.

Only needs additional storage for 1 bit per element of the matrix, compared to the full reallocation of the transpose() function. It is however somewhat slower (4-5x more time in our debug build).

Definition at line 146 of file utils/containers/matrix/operators.hpp.

triangular_index()

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.

See triangular_indices() for the opposite function, which also explains the details, and triangular_size() to calculate the maximal k that will occur in a trian Matrix of a given size n.

Parameters

i,j	Indices of the Matrix for which to calculate the linear index k.
n	Size of the quadratic Matrix, i.e., the row/column length.

Returns

Linear index k for the given i and j.

Definition at line 56 of file utils/containers/matrix/operators.cpp.

triangular_indices()

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.

Given an upper triangle Matrix of size n == 5

0  k0  k1  k2  k3
0   0  k4  k5  k6
0   0   0  k7  k8
0   0   0   0  k9
0   0   0   0   0

and given a k (like above), find the corresponding indices i and j for this k, e.g.,

k == 0 --> i == 0, j == 1
k == 5 --> i == 1, j == 3
k == 9 --> i == 3, j == 4
...

Because the calculation involves solving triangular numbers, the function internally operates on double values. This is a bit smelly, but seems to work (tested with n == 100,000).

See also triangular_index() for the opposite function, and triangular_size() to calculate the maximal k that will occur in a trian Matrix of a given size n.

Parameters

k	Linear index in the upper triangle of a quadratic Matrix.
n	Size of the quadratic Matrix, i.e., the row/column length.

Returns

Pair ( i, j ) of the indices for the given k.

Definition at line 44 of file utils/containers/matrix/operators.cpp.

triangular_size()

size_t triangular_size

(

size_t

n

)

Calculate the number of linear indices needed for a triangular Matrix of size n.

Given an upper triangle Matrix of size n == 5

0  k0  k1  k2  k3
0   0  k4  k5  k6
0   0   0  k7  k8
0   0   0   0  k9
0   0   0   0   0

we need 10 indices k == 0..9 to linearly describe the positions in the triangle. This function returns this number of indices for a given n.

See also triangular_indices() for calculating the Matrix indices i and j for a given k.

Parameters

n	Size of the quadratic Matrix, i.e., the row/column length.

Returns

Number of needed linear indices k to describe a triangle of the Matrix.

Definition at line 62 of file utils/containers/matrix/operators.cpp.

tridiagonal_ql_algorithm()

void tridiagonal_ql_algorithm	(	Matrix< double > &	data,
		TridiagonalDecompositionData &	tri,
		size_t	max_iterations = 1000
	)

Reduce a symmetric matrix to a symmetric tridiagonal matrix.

Uses the data and the intermediate result after executing reduce_to_tridiagonal_matrix() in order to run the algorithm. See there for details.

Both parameters are modified during the algorithm. After it is finished, tri.eigenvalues contains the eigenvalus and data the associated eigenvectors of the original data.

The implementation of this function is largely borrowed from http://www.classification-society.org/csna/mda-sw/pca.c published as Public Domain by Fionn Murtagh.

Parameters

data	Input data matrix. Operations are performed inline, that is, the matrix is changed during execution of the function.
tri	Tridiagonal matrix coming from reduce_to_tridiagonal_matrix().
max_iterations	Maximum number of iterations to perform, default is 1000. If set to 0, the algorithm continues until convergence. As convergence is not given for all data, this might result in an infinite loop.

Definition at line 160 of file pca.cpp.

trim()

std::string trim	(	std::string const &	s,
		std::string const &	delimiters
	)

Return a copy of the input string, with trimmed white spaces (or any other delimiters).

Definition at line 827 of file string.cpp.

trim_left()

std::string trim_left	(	std::string const &	s,
		std::string const &	delimiters
	)

Return a copy of the input string, with right trimmed white spaces (or any other delimiters).

Definition at line 815 of file string.cpp.

trim_right()

std::string trim_right	(	std::string const &	s,
		std::string const &	delimiters
	)

Return a copy of the input string, with left trimmed white spaces (or any other delimiters).

Definition at line 803 of file string.cpp.

udu_transpose_()

std::vector<double> genesis::utils::udu_transpose_	(	size_t	M,
		std::vector< double > const &	U,
		double	scale
	)

Calculate U.D.U-transpose.

For packed upper unit triangular matrix, U, and diagonal matrix D (occupying the same space, U), calculate U.D.U-transpose and scale it by a constant multiple.

Definition at line 618 of file glm.cpp.

udvdu_transpose_()

std::vector<double> genesis::utils::udvdu_transpose_	(	size_t	M,
		std::vector< double > const &	U,
		std::vector< double > const &	V,
		double	scale
	)

Calculate U.D.V.D.U-transpose.

For packed upper unit triangular matrix, U, and diagonal matrix D (occupying the same space, U), and packed symmetric matrix V, calculate U.D.V.D.U-transpose and multiply by a scale factor.

Definition at line 659 of file glm.cpp.

validate()

bool validate

(

Dataframe const &

df

)

Located in genesis/utils/containers/dataframe/operators.hpp

Definition at line 404 of file utils/containers/dataframe/operators.cpp.

weighted_arithmetic_mean() [1/2]

double genesis::utils::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.

The iterators first_value and last_value, as well as first_weight and last_weight, need to point to ranges of double values, with last_value and last_weight being the past-the-end elements. Both ranges need to have the same size. The function then calculates the weighted 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. The weights have to be non-negative.

See also

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

arithmetic_mean() for the unweighted version.

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

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

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

weighted_harmonic_mean() for a function that calculates the weighted harmonic mean.

Definition at line 496 of file statistics.hpp.

weighted_arithmetic_mean() [2/2]

double genesis::utils::weighted_arithmetic_mean ( std::vector< double > const &  values, std::vector< double > const &  weights  )

inline

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

See also

weighted_arithmetic_mean( ForwardIterator first, ForwardIterator last ) for details.

arithmetic_mean() for the unweighted version.

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

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

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

weighted_harmonic_mean() for a function that calculates the weighted harmonic mean.

Definition at line 547 of file statistics.hpp.

weighted_geometric_mean() [1/2]

double genesis::utils::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.

The iterators first_value and last_value, as well as first_weight and last_weight, need to point to ranges of double values, with last_value and last_weight being the past-the-end elements. Both ranges need to have the same size. The function then calculates the weighted geometric mean of all positive 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. If finite non-positive numbers (zero or negative) are found, an exception is thrown. The weights have to be non-negative.

For a set of values \( v \) and a set of weights \( w \), the weighted geometric mean \( g \) is calculated following [1]:

\( g = \exp \left( \frac{ \sum w \cdot \log v }{ \sum w } \right) \)

That is, if all weights are 1.0, the formula yields the standard geometric mean.

[1] J. D. Silverman, A. D. Washburne, S. Mukherjee, and L. A. David, "A phylogenetic transform enhances analysis of compositional microbiota data," Elife, vol. 6, p. e21887, Feb. 2017. https://elifesciences.org/articles/21887

See also

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

geometric_mean() for the unweighted version.

arithmetic_mean() for a function that calculates the arithmetic mean, and

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

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

weighted_harmonic_mean() for a function that calculates the weighted harmonic mean.

Definition at line 649 of file statistics.hpp.

weighted_geometric_mean() [2/2]

double genesis::utils::weighted_geometric_mean ( std::vector< double > const &  values, std::vector< double > const &  weights  )

inline

Calculate the weighted geometric mean of a std::vector of double elements.

See also

weighted_geometric_mean( ForwardIterator first, ForwardIterator last ) for details.

geometric_mean() for the unweighted version.

arithmetic_mean() for a function that calculates the arithmetic mean, and

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

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

weighted_harmonic_mean() for a function that calculates the weighted harmonic mean.

Definition at line 706 of file statistics.hpp.

weighted_harmonic_mean() [1/2]

double genesis::utils::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.

The iterators first_value and last_value, as well as first_weight and last_weight, need to point to ranges of double values, with last_value and last_weight being the past-the-end elements. Both ranges need to have the same size. The function then calculates the weighted harmonic mean of all non-negative or positive (depending on the zero_policy) 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. If finite negative numbers are found, an exception is thrown. Zero values are treated according to the zero_policy. The weights have to be non-negative, and elements with non-finite weights are skipped.

For a set of values \( v \) and a set of weights \( w \), the weighted harmonic mean \( g \) is calculated following [1]:

\( h = \frac{ \sum w }{ \sum \frac{ w }{ v } } \)

That is, if all weights are 1.0, the formula yields the standard harmonic mean.

See also

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

harmonic_mean() for the unweighted version.

arithmetic_mean() for a function that calculates the arithmetic mean, and

geometric_mean() for a function that calculates the geometric mean.

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

weighted_geometric_mean() for a function that calculates the weighted geometric mean.

Definition at line 884 of file statistics.hpp.

weighted_harmonic_mean() [2/2]

double genesis::utils::weighted_harmonic_mean ( std::vector< double > const &  values, std::vector< double > const &  weights, HarmonicMeanZeroPolicy  zero_policy = HarmonicMeanZeroPolicy::kThrow  )

inline

Calculate the weighted harmonic mean of a std::vector of double elements.

See also

weighted_harmonic_mean( ForwardIterator first, ForwardIterator last ) for details.

harmonic_mean() for the unweighted version.

arithmetic_mean() for a function that calculates the arithmetic mean, and

geometric_mean() for a function that calculates the geometric mean.

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

weighted_geometric_mean() for a function that calculates the weighted geometric mean.

Definition at line 988 of file statistics.hpp.

weighted_inner_product()

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.

The weights can be empty, in which case the simple inner product of x_input and y_input is returned.

Definition at line 322 of file utils/math/regression/helper.cpp.

weighted_mean_centering()

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.

If centering is false, write y_output to contain the (strata) (weighted) means. If centering is true, center the input y_input around these means, i.e., calculaute either the "fitted value" or the residual from a model in which only strata are fitted.

The weights and strata can be empty. y_input and y_output can be the same vector.

Definition at line 71 of file utils/math/regression/helper.cpp.

weighted_residuals()

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.

The weights can be empty. The results are written to y_output. y_input and y_output can be the same vector. Returns the regression coefficient.

Definition at line 221 of file utils/math/regression/helper.cpp.

weighted_sum()

double weighted_sum	(	std::vector< double > const &	x_input,
		std::vector< double > const &	weights = std::vector< double >{}
	)

(Weighted) sum of a vector of values.

The weights can be empty, in which case the simple sum of x_input is returned.

Definition at line 364 of file utils/math/regression/helper.cpp.

weighted_sum_of_squares()

double weighted_sum_of_squares	(	std::vector< double > const &	x_input,
		std::vector< double > const &	weights = std::vector< double >{}
	)

(Weighted) sum of squares.

The weights can be empty, in which case the simple sum of squares of x_input is returned.

Definition at line 290 of file utils/math/regression/helper.cpp.

wrap()

std::string wrap	(	std::string const &	text,
		size_t	line_length
	)

Wrap a text at a given line_length.

Definition at line 680 of file string.cpp.

xgetbv()

uint64_t genesis::utils::xgetbv

(

unsigned int

index

)

Definition at line 485 of file info.cpp.

xml_attribute()

std::string genesis::utils::xml_attribute	(	std::string const &	name,
		T const &	value
	)

Definition at line 52 of file utils/formats/xml/helper.hpp.

xml_comment()

std::string xml_comment

(

std::string const &

content

)

Definition at line 70 of file utils/formats/xml/helper.cpp.

xml_deescape()

std::string xml_deescape

(

std::string const &

txt

)

De-escape special XML characters.

Definition at line 59 of file utils/formats/xml/helper.cpp.

xml_escape()

std::string xml_escape

(

std::string const &

txt

)

Escape special XML characters.

Definition at line 45 of file utils/formats/xml/helper.cpp.

xml_value_to_comment()

const XmlComment * xml_value_to_comment

(

const XmlValue *

v

)

Converts a pointer to an XmlValue to XmlComment if appropriate.

Throws if the dynamic type of the object is not actually an XmlComment object.

Definition at line 47 of file xml/document.cpp.

xml_value_to_element()

const XmlElement * xml_value_to_element

(

const XmlValue *

v

)

Converts a pointer to an XmlValue to XmlElement if appropriate.

Throws if the dynamic type of the object is not actually an XmlElement object.

Definition at line 77 of file xml/document.cpp.

xml_value_to_markup()

const XmlMarkup * xml_value_to_markup

(

const XmlValue *

v

)

Converts a pointer to an XmlValue to XmlMarkup if appropriate.

Throws if the dynamic type of the object is not actually an XmlMarkup object.

Definition at line 62 of file xml/document.cpp.

Typedef Documentation

DefaultIntervalNumericalType

using DefaultIntervalNumericalType = int

Default numerical type to use in an Interval.

Definition at line 61 of file interval.hpp.

InputReader

using InputReader = AsynchronousReader

Alias for the either AsynchronousReader or SynchronousReader.

This typedef is an alias for AsynchronousReader. We use it in order to be able to easily switch to using SynchronousReader, by aliasing that instead. However, as of now, we always use the AsynchronousReader throughout all reading functionality, for efficiency reasons.

Definition at line 61 of file input_reader.hpp.

KahanSum

using KahanSum = CompensatedSum<KahanSummation>

Typedef shorthand for a Kahan sum.

Definition at line 69 of file compensated_sum.hpp.

KleinSum

using KleinSum = CompensatedSum<KleinSummation>

Typedef shorthand for a Kahan Babushka Klein sum.

Definition at line 79 of file compensated_sum.hpp.

NamedColorList

using NamedColorList = std::vector<std::pair<std::string, ColorBytes> >

Definition at line 59 of file names.cpp.

NeumaierSum

using NeumaierSum = CompensatedSum<NeumaierSummation>

Typedef shorthand for a Kahan Babushka Neumaier sum.

Definition at line 74 of file compensated_sum.hpp.

Enumeration Type Documentation

ColorListDiverging

enum ColorListDiverging

strong

Enumerator
kBrbg
kPiyg
kPrgn
kPuor
kRdbu
kRdgy
kRdylbu
kRdylgn
kSpectral

Definition at line 136 of file list_diverging.hpp.

ColorListMisc

enum ColorListMisc

strong

Enumerator
kNextstrain

Definition at line 91 of file list_misc.hpp.

ColorListQualitative

enum ColorListQualitative

strong

Enumerator
kAccent
kDark2
kPaired
kPastel1
kPastel2
kSet1
kSet2
kSet3

Definition at line 127 of file list_qualitative.hpp.

ColorListSequential

enum ColorListSequential

strong

Enumerator
kBupubk
kBlues
kBugn
kBupu
kGnbu
kGreens
kGreys
kOranges
kOrrd
kPubu
kPubugn
kPurd
kPurples
kRdpu
kReds
kYlgn
kYlgnbu
kYlorbr
kYlorrd
kHeat
kMagma
kInferno
kPlasma
kViridis

Definition at line 262 of file list_sequential.hpp.

GeoCoordinateComponent

enum GeoCoordinateComponent

strong

Local helper enum that indicates which component of a coordinate we are dealing with.

Enumerator
kLatitude
kLongitude

Definition at line 57 of file utils/tools/geodesy/functions.cpp.

GzipCompressionLevel

enum GzipCompressionLevel : int

strong

List of possible compression levels used for GzipOStream.

The compression levels are handed over to zlib for compression, which currently allows all values between 1 (best speed) and 9 (best compression), with the special case 0 (no compression), as well as -1 for the default compression. Currently, the zlib default compression level corresponds to level 6, as this is a good compromise between speed and compression (it forms the "elbow" of the curve), hence we also use this as our default level.

The enum only lists those four special levels. However, we use a fixed enum here (with the underlying type int), meaning that all values in between 1 and 9 are also allowed to be used. Values outside of the range [-1, 9] will lead to an exception being thrown when used in GzipOStream.

See also

GzipOStream

GzipOFStream

Enumerator
kDefaultCompression
kNoCompression
kBestSpeed
kBestCompression

Definition at line 100 of file gzip_stream.hpp.

HarmonicMeanZeroPolicy

enum HarmonicMeanZeroPolicy

strong

Select a policy on how to treat zeroes in the computation of harmonic_mean() and weighted_harmonic_mean().

Enumerator
kThrow	Throw an exception when a zero value is encountered in the data.
kIgnore	Ignore any zero values.
kReturnZero	If any zero value is encountered in the data, simply return zero as the harmonic mean. This is for example the interpretation of using the harmonic mean to compute the average resistance of a set of resistors in parallel, where one zero-resistance resistor would lead to the whole set having zero resistance.
kCorrection	Apply a zero-value correction. The correction is computed as \( \mu_h = \frac{N_T - N_0}{\sum^{N_T - N_0}_{i=1} \frac{1}{x_i}} \times \frac{N_T - N_0} {N_T} \) where \( \mu_h \) is harmonic mean, \( x_i \) are the non-zero values of the data only, \( N_T \) is the (total) sample size, and \( N_0 \) is the number of zero values. This follows the EPA (Environmental Protection Agency) program DFLOW, see https://www.epa.gov/ceam/dflow and https://rdrr.io/cran/lmomco/man/harmonic.mean.html

Definition at line 721 of file statistics.hpp.

HashingFunctions

enum HashingFunctions

strong

List of the currently implemented hashing functions.

This is useful in order to select the used hashing function at runtime for some algorithms.

See also

hash_hex()

Enumerator
kMD5	Use MD5 for hashing.
kSHA1	Use SHA1 for hashing.
kSHA256	Use SHA256 for hashing.

Definition at line 53 of file utils/tools/hash/functions.hpp.

KendallsTauMethod

enum KendallsTauMethod

strong

Method for computing Kendall's Tau.

See kendalls_tau_correlation_coefficient() for the function that uses this. See https://en.wikipedia.org/wiki/Kendall_rank_correlation_coefficient and https://docs.scipy.org/doc/scipy-1.12.0/reference/generated/scipy.stats.kendalltau.html#scipy.stats.kendalltau for details on the different methods.

Enumerator
kTauA	Compute Tau-a, which does not make any adjustment for ties.
kTauB	Compute Tau-b, which does adjustments for ties.
kTauC	Compute Tau-c, (also called Stuart-Kendall Tau-c).

Definition at line 187 of file correlation.hpp.

KmeansInitializationStrategy

enum KmeansInitializationStrategy

strong

Enum of the initialization strategies offered by the Kmeans implementation.

Enumerator
kRandomAssignments
kRandomCentroids
kKmeansPlusPlus
kNone

Definition at line 64 of file utils/math/kmeans.hpp.

MdsAlgorithm

enum MdsAlgorithm

strong

Choice of algorithm to use for Multi-Dimensional Scaling (MDS).

See also

multi_dimensional_scaling() for details on the function and for the license.

More information is avaialbe in the Acknowledgements.

Enumerator
kUcf	Use the UCF implementation (recommended). This is a re-implementation of Laurens van der Maaten's MDS in his Matlab Toolbox for Dimensionality Reduction.
kSmacof	Use the SMACOF implementation. This is a re-implementation of Michael Bronstein's SMACOF in his Matlab Toolbox for Surface Comparison and Analysis.

Definition at line 52 of file mds.hpp.

PcaStandardization

enum PcaStandardization

strong

Setting for principal_component_analysis() to determine which form of standardization of the data to use prior to perfoming the PCA.

Enumerator
kCorrelation	Standardize the mean and variance of the data before performing the PCA. Best to use when the data has widely varying scales in between the columns, i.e., if the columns present data from different domains. Also, see correlation_matrix().
kCovariance	Standardize the mean, but not the variance of the data before performing the PCA. Best to use when the data has similar scales in between the columns, i.e., if the columns present data from the same domain. Also, see covariance_matrix().
kSSCP	Do not perform any standardization prior to performing the PCA. Not recommended. Also, see sums_of_squares_and_cross_products_matrix().

Definition at line 49 of file pca.hpp.

RedBackColor

enum RedBackColor

strong

Definition for Red-Black Tree coloring.

Used in IntervalTree and IntervalTreeNode.

Enumerator
kInvalid
kRed
kBlack
kKDoubleBlack

Definition at line 65 of file utils/containers/interval_tree/node.hpp.

SkipWhitespace

enum SkipWhitespace : unsigned char

strong

Option to determine how to treat surrounding whitespace when scanning an input stream.

This helper enum is used in the input stream scanner functions read_char_or_throw() and affirm_char_or_throw() in order to indicate how they treat whitespace while looking for chars.

For checking whether a partcular option is set, it is possible to use the binary and operator &:

if( option & SkipWhitespace::kTrailing ) {
    // ...
}

Of course, simply comparing the values also works.

Enumerator
kNone	Skip no whitespace. Thus, immediately treat the current input char.
kLeading	Skip all whitespace in the input stream, then treat the next non-white char.
kTrailing	Treat the current char in the input stream, then skip the following whitespace.
kSurrounding	Skip whitespace, treat the first non-white char, then skip all following whitespace.

Definition at line 62 of file scanner.hpp.

Variable Documentation

ascii_names_

const std::array<std::string, 128> ascii_names_

static

List of all ASCII names.

We use this for extra clear user output, in order to make sure that the symbols can be understood when a parser finds an unexpected char.

List from "ASCII / ISO 8859-1 (Latin-1) Table with HTML Entity Names", see https://cs.stanford.edu/people/miles/iso8859.html

Definition at line 76 of file char.cpp.

ascii_symbols_

const std::array<std::string, 128> ascii_symbols_

static

Initial value:

= {{
    "NUL", "SOH", "STX", "ETX", "EOT", "ENQ", "ACK", "BEL", "BS", "HT", "LF", "VT", "FF", "CR", "SO", "SI",
    "DLE", "DC1", "DC2", "DC3", "DC4", "NAK", "SYN", "ETB", "CAN", "EM", "SUB", "ESC", "FS", "GS", "RS", "US",
    " ", "!", "\"", "#", "$", "%", "&", "'", "(", ")", "*", "+", ",", "-", ".", "/",
    "0", "1", "2", "3", "4", "5", "6", "7", "8", "9", ":", ";", "<", "=", ">", "?",
    "@", "A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K", "L", "M", "N", "O",
    "P", "Q", "R", "S", "T", "U", "V", "W", "X", "Y", "Z", "[", "\\", "]", "^", "_",
    "`", "a", "b", "c", "d", "e", "f", "g", "h", "i", "j", "k", "l", "m", "n", "o",
    "p", "q", "r", "s", "t", "u", "v", "w", "x", "y", "z", "{", "|", "}", "~", "DEL"
}}

List of all ASCII symbols.

Actually, we only need that for the non-printable characters. All printable ones are prepresented by their ASCII code directly. But as there is the "DEL" symbol at the end, using this list is easier than introducing a special case for that.

Definition at line 56 of file char.cpp.

base64_encode_lookup_

const char base64_encode_lookup_[]

static

Initial value:

=
    "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/"

Definition at line 47 of file base64.cpp.

base64_pad_char_

const char base64_pad_char_ = '='

static

Definition at line 49 of file base64.cpp.

color_list_accent_

const std::vector<Color> color_list_accent_

Initial value:

= {{
    { 0.498039, 0.788235, 0.498039 }, 
    { 0.745098, 0.682353, 0.831373 }, 
    { 0.992157, 0.752941, 0.525490 }, 
    { 1.000000, 1.000000, 0.600000 }, 
    { 0.219608, 0.423529, 0.690196 }, 
    { 0.941176, 0.007843, 0.498039 }, 
    { 0.749020, 0.356863, 0.090196 }, 
    { 0.400000, 0.400000, 0.400000 }  
}}

Definition at line 56 of file list_qualitative.cpp.

color_list_blues_

const std::vector<Color> color_list_blues_

Initial value:

= {{
    { 0.968627, 0.984314, 1.000000 }, 
    { 0.870588, 0.921569, 0.968627 },
    { 0.776471, 0.858824, 0.937255 },
    { 0.619608, 0.792157, 0.882353 }, 
    { 0.419608, 0.682353, 0.839216 },
    { 0.258824, 0.572549, 0.776471 }, 
    { 0.129412, 0.443137, 0.709804 },
    { 0.031373, 0.317647, 0.611765 },
    { 0.031373, 0.188235, 0.419608 }  
}}

Definition at line 69 of file list_sequential.cpp.

color_list_brbg_

const std::vector<Color> color_list_brbg_

Initial value:

= {{
    { 0.329412, 0.188235, 0.019608 },
    { 0.549020, 0.317647, 0.039216 }, 
    { 0.749020, 0.505882, 0.176471 }, 
    { 0.874510, 0.760784, 0.490196 },
    { 0.964706, 0.909804, 0.764706 }, 
    { 0.960784, 0.960784, 0.960784 },
    { 0.780392, 0.917647, 0.898039 }, 
    { 0.501961, 0.803922, 0.756863 },
    { 0.207843, 0.592157, 0.560784 }, 
    { 0.003922, 0.400000, 0.368627 }, 
    { 0.000000, 0.235294, 0.188235 }
}}

Definition at line 56 of file list_diverging.cpp.

color_list_bugn_

const std::vector<Color> color_list_bugn_

Initial value:

= {{
    { 0.968627, 0.988235, 0.992157 }, 
    { 0.898039, 0.960784, 0.976471 },
    { 0.800000, 0.925490, 0.901961 },
    { 0.600000, 0.847059, 0.788235 }, 
    { 0.400000, 0.760784, 0.643137 },
    { 0.254902, 0.682353, 0.462745 }, 
    { 0.137255, 0.545098, 0.270588 },
    { 0.000000, 0.427451, 0.172549 },
    { 0.000000, 0.266667, 0.105882 }  
}}

Definition at line 81 of file list_sequential.cpp.

color_list_bupu_

const std::vector<Color> color_list_bupu_

Initial value:

= {{
    { 0.968627, 0.988235, 0.992157 }, 
    { 0.878431, 0.925490, 0.956863 },
    { 0.749020, 0.827451, 0.901961 },
    { 0.619608, 0.737255, 0.854902 }, 
    { 0.549020, 0.588235, 0.776471 },
    { 0.549020, 0.419608, 0.694118 }, 
    { 0.533333, 0.254902, 0.615686 },
    { 0.505882, 0.058824, 0.486275 },
    { 0.301961, 0.000000, 0.294118 }  
}}

Definition at line 93 of file list_sequential.cpp.

color_list_bupubk_

const std::vector<Color> color_list_bupubk_

Initial value:

= {{
    { 0.505882353, 0.749019608, 1.0 },         
    { 0.752941176, 0.250980392, 0.745098039 }, 
    { 0.0, 0.0, 0.0 }                          
}}

Our own color list used for visualizing trees.

Definition at line 50 of file list_sequential.cpp.

color_list_dark2_

const std::vector<Color> color_list_dark2_

Initial value:

= {{
    { 0.105882, 0.619608, 0.466667 }, 
    { 0.850980, 0.372549, 0.007843 }, 
    { 0.458824, 0.439216, 0.701961 }, 
    { 0.905882, 0.160784, 0.541176 }, 
    { 0.400000, 0.650980, 0.117647 }, 
    { 0.901961, 0.670588, 0.007843 }, 
    { 0.650980, 0.462745, 0.113725 }, 
    { 0.400000, 0.400000, 0.400000 }  
}}

Definition at line 67 of file list_qualitative.cpp.

color_list_gnbu_

const std::vector<Color> color_list_gnbu_

Initial value:

= {{
    { 0.968627, 0.988235, 0.941176 }, 
    { 0.878431, 0.952941, 0.858824 },
    { 0.800000, 0.921569, 0.772549 },
    { 0.658824, 0.866667, 0.709804 }, 
    { 0.482353, 0.800000, 0.768627 },
    { 0.305882, 0.701961, 0.827451 }, 
    { 0.168627, 0.549020, 0.745098 },
    { 0.031373, 0.407843, 0.674510 },
    { 0.031373, 0.250980, 0.505882 }  
}}

Definition at line 105 of file list_sequential.cpp.

color_list_greens_

const std::vector<Color> color_list_greens_

Initial value:

= {{
    { 0.968627, 0.988235, 0.960784 }, 
    { 0.898039, 0.960784, 0.878431 },
    { 0.780392, 0.913725, 0.752941 },
    { 0.631373, 0.850980, 0.607843 }, 
    { 0.454902, 0.768627, 0.462745 },
    { 0.254902, 0.670588, 0.364706 }, 
    { 0.137255, 0.545098, 0.270588 },
    { 0.000000, 0.427451, 0.172549 },
    { 0.000000, 0.266667, 0.105882 }  
}}

Definition at line 117 of file list_sequential.cpp.

color_list_greys_

const std::vector<Color> color_list_greys_

Initial value:

= {{
    { 1.000000, 1.000000, 1.000000 }, 
    { 0.941176, 0.941176, 0.941176 },
    { 0.850980, 0.850980, 0.850980 },
    { 0.741176, 0.741176, 0.741176 }, 
    { 0.588235, 0.588235, 0.588235 },
    { 0.450980, 0.450980, 0.450980 }, 
    { 0.321569, 0.321569, 0.321569 },
    { 0.145098, 0.145098, 0.145098 },
    { 0.000000, 0.000000, 0.000000 }  
}}

Definition at line 129 of file list_sequential.cpp.

color_list_heat_

const std::vector<Color> color_list_heat_

Initial value:

= {{
    { 1.000000, 1.000000, 1.000000 }, 
    { 1.000000, 1.000000, 0.500000 },
    { 1.000000, 1.000000, 0.000000 }, 
    { 1.000000, 0.800000, 0.000000 },
    { 1.000000, 0.600000, 0.000000 }, 
    { 1.000000, 0.400000, 0.000000 },
    { 1.000000, 0.200000, 0.000000 },
    { 1.000000, 0.000000, 0.000000 }  
}}

Definition at line 294 of file list_sequential.cpp.

color_list_inferno_

const std::vector<Color> color_list_inferno_

Definition at line 601 of file list_sequential.cpp.

color_list_lego_

const NamedColorList color_list_lego_

Struct that stores a static const map of named LEGO colors.

The map stores the color names of the LEGO colors from https://rebrickable.com/downloads/ as of 2024-06-17.

Definition at line 1187 of file names.cpp.

color_list_magma_

const std::vector<Color> color_list_magma_

Definition at line 330 of file list_sequential.cpp.

color_list_nextstrain_256_

const std::vector<Color> color_list_nextstrain_256_

static

Definition at line 197 of file list_misc.cpp.

color_list_oranges_

const std::vector<Color> color_list_oranges_

Initial value:

= {{
    { 1.000000, 0.960784, 0.921569 }, 
    { 0.996078, 0.901961, 0.807843 },
    { 0.992157, 0.815686, 0.635294 },
    { 0.992157, 0.682353, 0.419608 }, 
    { 0.992157, 0.552941, 0.235294 },
    { 0.945098, 0.411765, 0.074510 }, 
    { 0.850980, 0.282353, 0.003922 },
    { 0.650980, 0.211765, 0.011765 },
    { 0.498039, 0.152941, 0.015686 }  
}}

Definition at line 141 of file list_sequential.cpp.

color_list_orrd_

const std::vector<Color> color_list_orrd_

Initial value:

= {{
    { 1.000000, 0.968627, 0.925490 }, 
    { 0.996078, 0.909804, 0.784314 },
    { 0.992157, 0.831373, 0.619608 },
    { 0.992157, 0.733333, 0.517647 }, 
    { 0.988235, 0.552941, 0.349020 },
    { 0.937255, 0.396078, 0.282353 }, 
    { 0.843137, 0.188235, 0.121569 },
    { 0.701961, 0.000000, 0.000000 },
    { 0.498039, 0.000000, 0.000000 }  
}}

Definition at line 153 of file list_sequential.cpp.

color_list_paired_

const std::vector<Color> color_list_paired_

Initial value:

= {{
    { 0.650980, 0.807843, 0.890196 }, 
    { 0.121569, 0.470588, 0.705882 }, 
    { 0.698039, 0.874510, 0.541176 }, 
    { 0.200000, 0.627451, 0.172549 }, 
    { 0.984314, 0.603922, 0.600000 }, 
    { 0.890196, 0.101961, 0.109804 }, 
    { 0.992157, 0.749020, 0.435294 }, 
    { 1.000000, 0.498039, 0.000000 }, 
    { 0.792157, 0.698039, 0.839216 }, 
    { 0.415686, 0.239216, 0.603922 }, 
    { 1.000000, 1.000000, 0.600000 }, 
    { 0.694118, 0.349020, 0.156863 }  
}}

Definition at line 78 of file list_qualitative.cpp.

color_list_pastel1_

const std::vector<Color> color_list_pastel1_

Initial value:

= {{
    { 0.984314, 0.705882, 0.682353 }, 
    { 0.701961, 0.803922, 0.890196 }, 
    { 0.800000, 0.921569, 0.772549 }, 
    { 0.870588, 0.796078, 0.894118 }, 
    { 0.996078, 0.850980, 0.650980 }, 
    { 1.000000, 1.000000, 0.800000 }, 
    { 0.898039, 0.847059, 0.741176 }, 
    { 0.992157, 0.854902, 0.925490 }, 
    { 0.949020, 0.949020, 0.949020 }  
}}

Definition at line 93 of file list_qualitative.cpp.

color_list_pastel2_

const std::vector<Color> color_list_pastel2_

Initial value:

= {{
    { 0.701961, 0.886275, 0.803922 }, 
    { 0.992157, 0.803922, 0.674510 }, 
    { 0.803922, 0.709804, 0.909804 }, 
    { 0.956863, 0.792157, 0.894118 }, 
    { 0.839216, 0.960784, 0.788235 }, 
    { 1.000000, 0.949020, 0.682353 }, 
    { 0.945098, 0.886275, 0.800000 }, 
    { 0.800000, 0.800000, 0.800000 }  
}}

Definition at line 105 of file list_qualitative.cpp.

color_list_piyg_

const std::vector<Color> color_list_piyg_

Initial value:

= {{
    { 0.556863, 0.003922, 0.321569 },
    { 0.772549, 0.105882, 0.490196 }, 
    { 0.870588, 0.466667, 0.682353 }, 
    { 0.945098, 0.713725, 0.854902 },
    { 0.992157, 0.878431, 0.937255 }, 
    { 0.968627, 0.968627, 0.968627 },
    { 0.901961, 0.960784, 0.815686 }, 
    { 0.721569, 0.882353, 0.525490 },
    { 0.498039, 0.737255, 0.254902 }, 
    { 0.301961, 0.572549, 0.129412 }, 
    { 0.152941, 0.392157, 0.098039 }
}}

Definition at line 70 of file list_diverging.cpp.

color_list_plasma_

const std::vector<Color> color_list_plasma_

Definition at line 872 of file list_sequential.cpp.

color_list_prgn_

const std::vector<Color> color_list_prgn_

Initial value:

= {{
    { 0.250980, 0.000000, 0.294118 },
    { 0.462745, 0.164706, 0.513725 }, 
    { 0.600000, 0.439216, 0.670588 }, 
    { 0.760784, 0.647059, 0.811765 },
    { 0.905882, 0.831373, 0.909804 }, 
    { 0.968627, 0.968627, 0.968627 },
    { 0.850980, 0.941176, 0.827451 }, 
    { 0.650980, 0.858824, 0.627451 },
    { 0.352941, 0.682353, 0.380392 }, 
    { 0.105882, 0.470588, 0.215686 }, 
    { 0.000000, 0.266667, 0.105882 }
}}

Definition at line 84 of file list_diverging.cpp.

color_list_pubu_

const std::vector<Color> color_list_pubu_

Initial value:

= {{
    { 1.000000, 0.968627, 0.984314 }, 
    { 0.925490, 0.905882, 0.949020 },
    { 0.815686, 0.819608, 0.901961 },
    { 0.650980, 0.741176, 0.858824 }, 
    { 0.454902, 0.662745, 0.811765 },
    { 0.211765, 0.564706, 0.752941 }, 
    { 0.019608, 0.439216, 0.690196 },
    { 0.015686, 0.352941, 0.552941 },
    { 0.007843, 0.219608, 0.345098 }  
}}

Definition at line 165 of file list_sequential.cpp.

color_list_pubugn_

const std::vector<Color> color_list_pubugn_

Initial value:

= {{
    { 1.000000, 0.968627, 0.984314 }, 
    { 0.925490, 0.886275, 0.941176 },
    { 0.815686, 0.819608, 0.901961 },
    { 0.650980, 0.741176, 0.858824 }, 
    { 0.403922, 0.662745, 0.811765 },
    { 0.211765, 0.564706, 0.752941 }, 
    { 0.007843, 0.505882, 0.541176 },
    { 0.003922, 0.423529, 0.349020 },
    { 0.003922, 0.274510, 0.211765 }  
}}

Definition at line 177 of file list_sequential.cpp.

color_list_puor_

const std::vector<Color> color_list_puor_

Initial value:

= {{
    { 0.498039, 0.231373, 0.031373 },
    { 0.701961, 0.345098, 0.023529 }, 
    { 0.878431, 0.509804, 0.078431 }, 
    { 0.992157, 0.721569, 0.388235 },
    { 0.996078, 0.878431, 0.713725 }, 
    { 0.968627, 0.968627, 0.968627 },
    { 0.847059, 0.854902, 0.921569 }, 
    { 0.698039, 0.670588, 0.823529 },
    { 0.501961, 0.450980, 0.674510 }, 
    { 0.329412, 0.152941, 0.533333 }, 
    { 0.176471, 0.000000, 0.294118 }
}}

Definition at line 98 of file list_diverging.cpp.

color_list_purd_

const std::vector<Color> color_list_purd_

Initial value:

= {{
    { 0.968627, 0.956863, 0.976471 }, 
    { 0.905882, 0.882353, 0.937255 },
    { 0.831373, 0.725490, 0.854902 },
    { 0.788235, 0.580392, 0.780392 }, 
    { 0.874510, 0.396078, 0.690196 },
    { 0.905882, 0.160784, 0.541176 }, 
    { 0.807843, 0.070588, 0.337255 },
    { 0.596078, 0.000000, 0.262745 },
    { 0.403922, 0.000000, 0.121569 }  
}}

Definition at line 189 of file list_sequential.cpp.

color_list_purples_

const std::vector<Color> color_list_purples_

Initial value:

= {{
    { 0.988235, 0.984314, 0.992157 }, 
    { 0.937255, 0.929412, 0.960784 },
    { 0.854902, 0.854902, 0.921569 },
    { 0.737255, 0.741176, 0.862745 }, 
    { 0.619608, 0.603922, 0.784314 },
    { 0.501961, 0.490196, 0.729412 }, 
    { 0.415686, 0.317647, 0.639216 },
    { 0.329412, 0.152941, 0.560784 },
    { 0.247059, 0.000000, 0.490196 }  
}}

Definition at line 201 of file list_sequential.cpp.

color_list_rdbu_

const std::vector<Color> color_list_rdbu_

Initial value:

= {{
    { 0.403922, 0.000000, 0.121569 },
    { 0.698039, 0.094118, 0.168627 }, 
    { 0.839216, 0.376471, 0.301961 }, 
    { 0.956863, 0.647059, 0.509804 },
    { 0.992157, 0.858824, 0.780392 }, 
    { 0.968627, 0.968627, 0.968627 },
    { 0.819608, 0.898039, 0.941176 }, 
    { 0.572549, 0.772549, 0.870588 },
    { 0.262745, 0.576471, 0.764706 }, 
    { 0.129412, 0.400000, 0.674510 }, 
    { 0.019608, 0.188235, 0.380392 }
}}

Definition at line 112 of file list_diverging.cpp.

color_list_rdgy_

const std::vector<Color> color_list_rdgy_

Initial value:

= {{
    { 0.403922, 0.000000, 0.121569 },
    { 0.698039, 0.094118, 0.168627 }, 
    { 0.839216, 0.376471, 0.301961 }, 
    { 0.956863, 0.647059, 0.509804 },
    { 0.992157, 0.858824, 0.780392 }, 
    { 1.000000, 1.000000, 1.000000 },
    { 0.878431, 0.878431, 0.878431 }, 
    { 0.729412, 0.729412, 0.729412 },
    { 0.529412, 0.529412, 0.529412 }, 
    { 0.301961, 0.301961, 0.301961 }, 
    { 0.101961, 0.101961, 0.101961 }
}}

Definition at line 126 of file list_diverging.cpp.

color_list_rdpu_

const std::vector<Color> color_list_rdpu_

Initial value:

= {{
    { 1.000000, 0.968627, 0.952941 }, 
    { 0.992157, 0.878431, 0.866667 },
    { 0.988235, 0.772549, 0.752941 },
    { 0.980392, 0.623529, 0.709804 }, 
    { 0.968627, 0.407843, 0.631373 },
    { 0.866667, 0.203922, 0.592157 }, 
    { 0.682353, 0.003922, 0.494118 },
    { 0.478431, 0.003922, 0.466667 },
    { 0.286275, 0.000000, 0.415686 }  
}}

Definition at line 213 of file list_sequential.cpp.

color_list_rdylbu_

const std::vector<Color> color_list_rdylbu_

Initial value:

= {{
    { 0.647059, 0.000000, 0.149020 },
    { 0.843137, 0.188235, 0.152941 }, 
    { 0.956863, 0.427451, 0.262745 }, 
    { 0.992157, 0.682353, 0.380392 },
    { 0.996078, 0.878431, 0.564706 }, 
    { 1.000000, 1.000000, 0.749020 },
    { 0.878431, 0.952941, 0.972549 }, 
    { 0.670588, 0.850980, 0.913725 },
    { 0.454902, 0.678431, 0.819608 }, 
    { 0.270588, 0.458824, 0.705882 }, 
    { 0.192157, 0.211765, 0.584314 }
}}

Definition at line 140 of file list_diverging.cpp.

color_list_rdylgn_

const std::vector<Color> color_list_rdylgn_

Initial value:

= {{
    { 0.647059, 0.000000, 0.149020 },
    { 0.843137, 0.188235, 0.152941 }, 
    { 0.956863, 0.427451, 0.262745 }, 
    { 0.992157, 0.682353, 0.380392 }, 
    { 0.996078, 0.878431, 0.545098 }, 
    { 1.000000, 1.000000, 0.749020 },
    { 0.850980, 0.937255, 0.545098 }, 
    { 0.650980, 0.850980, 0.415686 }, 
    { 0.400000, 0.741176, 0.388235 }, 
    { 0.101961, 0.596078, 0.313725 }, 
    { 0.000000, 0.407843, 0.215686 }
}}

Definition at line 154 of file list_diverging.cpp.

color_list_reds_

const std::vector<Color> color_list_reds_

Initial value:

= {{
    { 1.000000, 0.960784, 0.941176 }, 
    { 0.996078, 0.878431, 0.823529 },
    { 0.988235, 0.733333, 0.631373 },
    { 0.988235, 0.572549, 0.447059 }, 
    { 0.984314, 0.415686, 0.290196 },
    { 0.937255, 0.231373, 0.172549 }, 
    { 0.796078, 0.094118, 0.113725 },
    { 0.647059, 0.058824, 0.082353 },
    { 0.403922, 0.000000, 0.050980 }  
}}

Definition at line 225 of file list_sequential.cpp.

color_list_set1_

const std::vector<Color> color_list_set1_

Initial value:

= {{
    { 0.894118, 0.101961, 0.109804 }, 
    { 0.215686, 0.494118, 0.721569 }, 
    { 0.301961, 0.686275, 0.290196 }, 
    { 0.596078, 0.305882, 0.639216 }, 
    { 1.000000, 0.498039, 0.000000 }, 
    { 1.000000, 1.000000, 0.200000 }, 
    { 0.650980, 0.337255, 0.156863 }, 
    { 0.968627, 0.505882, 0.749020 }, 
    { 0.600000, 0.600000, 0.600000 }  
}}

Definition at line 116 of file list_qualitative.cpp.

color_list_set2_

const std::vector<Color> color_list_set2_

Initial value:

= {{
    { 0.400000, 0.760784, 0.647059 }, 
    { 0.988235, 0.552941, 0.384314 }, 
    { 0.552941, 0.627451, 0.796078 }, 
    { 0.905882, 0.541176, 0.764706 }, 
    { 0.650980, 0.847059, 0.329412 }, 
    { 1.000000, 0.850980, 0.184314 }, 
    { 0.898039, 0.768627, 0.580392 }, 
    { 0.701961, 0.701961, 0.701961 }  
}}

Definition at line 128 of file list_qualitative.cpp.

color_list_set3_

const std::vector<Color> color_list_set3_

Initial value:

= {{
    { 0.552941, 0.827451, 0.780392 }, 
    { 1.000000, 1.000000, 0.701961 }, 
    { 0.745098, 0.729412, 0.854902 }, 
    { 0.984314, 0.501961, 0.447059 }, 
    { 0.501961, 0.694118, 0.827451 }, 
    { 0.992157, 0.705882, 0.384314 }, 
    { 0.701961, 0.870588, 0.411765 }, 
    { 0.988235, 0.803922, 0.898039 }, 
    { 0.850980, 0.850980, 0.850980 }, 
    { 0.737255, 0.501961, 0.741176 }, 
    { 0.800000, 0.921569, 0.772549 }, 
    { 1.000000, 0.929412, 0.435294 }  
}}

Definition at line 139 of file list_qualitative.cpp.

color_list_spectral_

const std::vector<Color> color_list_spectral_

Initial value:

= {{
    { 0.61960784313725492, 0.003921568627450980, 0.25882352941176473 },
    { 0.83529411764705885, 0.24313725490196078 , 0.30980392156862746 },
    { 0.95686274509803926, 0.42745098039215684 , 0.2627450980392157  },
    { 0.99215686274509807, 0.68235294117647061 , 0.38039215686274508 },
    { 0.99607843137254903, 0.8784313725490196  , 0.54509803921568623 },
    { 1.0                , 1.0                 , 0.74901960784313726 },
    { 0.90196078431372551, 0.96078431372549022 , 0.59607843137254901 },
    { 0.6705882352941176 , 0.8666666666666667  , 0.64313725490196083 },
    { 0.4                , 0.76078431372549016 , 0.6470588235294118  },
    { 0.19607843137254902, 0.53333333333333333 , 0.74117647058823533 },
    { 0.36862745098039218, 0.30980392156862746 , 0.63529411764705879 }
}}

Definition at line 168 of file list_diverging.cpp.

color_list_viridis_

const std::vector<Color> color_list_viridis_

Definition at line 1143 of file list_sequential.cpp.

color_list_web_

const NamedColorList color_list_web_

Struct that stores a static const map of named web colors.

The map stores all 140 color names of the HTML web colors. It is mainly used as a simple way to create a color scheme in form of a vector of colors.

Definition at line 71 of file names.cpp.

color_list_xkcd_

const NamedColorList color_list_xkcd_

Struct that stores a static const map of named xkcd colors.

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.

Definition at line 225 of file names.cpp.

color_list_ylgn_

const std::vector<Color> color_list_ylgn_

Initial value:

= {{
    { 1.000000, 1.000000, 0.898039 }, 
    { 0.968627, 0.988235, 0.725490 },
    { 0.850980, 0.941176, 0.639216 },
    { 0.678431, 0.866667, 0.556863 }, 
    { 0.470588, 0.776471, 0.474510 },
    { 0.254902, 0.670588, 0.364706 }, 
    { 0.137255, 0.517647, 0.262745 },
    { 0.000000, 0.407843, 0.215686 },
    { 0.000000, 0.270588, 0.160784 }  
}}

Definition at line 237 of file list_sequential.cpp.

color_list_ylgnbu_

const std::vector<Color> color_list_ylgnbu_

Initial value:

= {{
    { 1.000000, 1.000000, 0.850980 }, 
    { 0.929412, 0.972549, 0.694118 },
    { 0.780392, 0.913725, 0.705882 },
    { 0.498039, 0.803922, 0.733333 }, 
    { 0.254902, 0.713725, 0.768627 },
    { 0.113725, 0.568627, 0.752941 }, 
    { 0.133333, 0.368627, 0.658824 },
    { 0.145098, 0.203922, 0.580392 },
    { 0.031373, 0.113725, 0.345098 }  
}}

Definition at line 249 of file list_sequential.cpp.

color_list_ylorbr_

const std::vector<Color> color_list_ylorbr_

Initial value:

= {{
    { 1.000000, 1.000000, 0.898039 }, 
    { 1.000000, 0.968627, 0.737255 },
    { 0.996078, 0.890196, 0.568627 },
    { 0.996078, 0.768627, 0.309804 }, 
    { 0.996078, 0.600000, 0.160784 },
    { 0.925490, 0.439216, 0.078431 }, 
    { 0.800000, 0.298039, 0.007843 },
    { 0.600000, 0.203922, 0.015686 },
    { 0.400000, 0.145098, 0.023529 }  
}}

Definition at line 261 of file list_sequential.cpp.

color_list_ylorrd_

const std::vector<Color> color_list_ylorrd_

Initial value:

= {{
    { 1.000000, 1.000000, 0.800000 }, 
    { 1.000000, 0.929412, 0.627451 },
    { 0.996078, 0.850980, 0.462745 }, 
    { 0.996078, 0.698039, 0.298039 },
    { 0.992157, 0.552941, 0.235294 },
    { 0.988235, 0.305882, 0.164706 }, 
    { 0.890196, 0.101961, 0.109804 },
    { 0.694118, 0.000000, 0.149020 }, 
}}

Definition at line 273 of file list_sequential.cpp.

color_lists_nextstrain_1_16_

const std::vector<std::vector<Color> > color_lists_nextstrain_1_16_

static

Definition at line 58 of file list_misc.cpp.

EARTH_MEAN_RADIUS

constexpr double EARTH_MEAN_RADIUS = 6371.0

constexpr

Earth is not flat!

Definition at line 49 of file utils/tools/geodesy/functions.hpp.

formats_

const std::array<std::string, 9> formats_

static

Initial value:

= {{
    "%Y-%m-%d", "%Y%m%d", "%Y-%m-%dT%H:%M:%S", "%Y-%m-%d %H:%M:%S", "%Y%m%dT%H%M%S",
    "%Y%m%d %H%M%S", "%Y%m%d%H%M%S", "%H:%M:%S", "%H%M%S"
}}

Definition at line 231 of file date_time.cpp.

genesis_log_mutex_

std::mutex genesis_log_mutex_

static

Definition at line 54 of file logging.cpp.

GZIP_DEFAULT_BUFFER_SIZE

const std::size_t GZIP_DEFAULT_BUFFER_SIZE = (std::size_t) 1 << 20

static

Default buffer size for all gzip (de)compression buffers.

See also

GzipIStream

GzipOStream

GzipIFStream

GzipOFStream

Definition at line 116 of file gzip_stream.hpp.

locales_

const std::array<std::string, 3> locales_ = {{ "C", "en_US.UTF-8", "" }}

static

Definition at line 228 of file date_time.cpp.

log_factorial_lookup_

const std::array<double, 1024> log_factorial_lookup_

static

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.

Definition at line 78 of file binomial.cpp.

MDS_EPSILON

constexpr double MDS_EPSILON = 0.0000001

constexpr

Definition at line 61 of file mds.cpp.

nullopt

const nullopt_t nullopt((nullopt_t::init()))

Optional to indicate an empty value.

pcg32_increment

const uint64_t pcg32_increment = 1442695040888963407u

static

Definition at line 51 of file random.cpp.

pcg32_multiplier

const uint64_t pcg32_multiplier = 6364136223846793005u

static

Definition at line 50 of file random.cpp.

pcg32_state

uint64_t pcg32_state = 0x4d595df4d0f33173

static

Definition at line 49 of file random.cpp.

PI

constexpr double PI = 3.141592653589793238463

constexpr

Make the world go round.

Definition at line 55 of file common.hpp.

tm_mutex_

std::mutex tm_mutex_

static

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.

Caveat: Currently, this file is the only place where we use std::localtime and std::gmtime. If this changes later, we might want to move this mutex to be available for other usages as well.

Definition at line 62 of file date_time.cpp.