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 ®ex="") |
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 ®ex, 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 ®ex="") |
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 ®ex="") |
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 ¶meters) |
template<class ColorNorm > | |
Matrix< utils::Color > | heat_map_matrix_range_all_ (Matrix< double > const &values, HeatmapParameters const ¶meters) |
template<class ColorNorm > | |
Matrix< utils::Color > | heat_map_matrix_range_col_ (Matrix< double > const &values, HeatmapParameters const ¶meters) |
template<class ColorNorm > | |
Matrix< utils::Color > | heat_map_matrix_range_row_ (Matrix< double > const &values, HeatmapParameters const ¶meters) |
MinMaxPair< double > | heat_map_matrix_update_min_max_ (MinMaxPair< double > const &min_max, HeatmapParameters const ¶meters) |
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 ¶meters) |
Matrix< Color > | make_heatmap_matrix (Matrix< double > const &values, HeatmapParameters const ¶meters) |
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 ×, 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 ×, 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... | |
|
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.
|
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.
|
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.
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
Definition at line 216 of file distance.hpp.
|
inline |
Calculate the Aitchison norm of a std::vector
of double
elements.
Definition at line 262 of file distance.hpp.
|
inline |
Check whether two doubles are almost equal, using a relative epsilon to compare them.
Definition at line 157 of file common.hpp.
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.
std::vector
. Definition at line 438 of file statistics.hpp.
|
inline |
Calculate the arithmetic mean of a std::vector
of double
elements.
Definition at line 473 of file statistics.hpp.
|
inline |
Sort two values in ascending order, inplace.
Definition at line 70 of file common.hpp.
T genesis::utils::base64_decode_ | ( | std::string const & | input | ) |
Definition at line 152 of file base64.cpp.
std::string base64_decode_string | ( | std::string const & | input | ) |
Definition at line 283 of file base64.cpp.
std::vector< std::uint8_t > base64_decode_uint8 | ( | std::string const & | input | ) |
Definition at line 277 of file base64.cpp.
std::string base64_encode | ( | std::string const & | input, |
size_t | line_length | ||
) |
Definition at line 272 of file base64.cpp.
std::string base64_encode | ( | std::vector< std::uint8_t > const & | input, |
size_t | line_length | ||
) |
Definition at line 267 of file base64.cpp.
std::string genesis::utils::base64_encode_ | ( | T const & | input, |
size_t | line_length | ||
) |
Definition at line 52 of file base64.cpp.
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.
|
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.
|
inline |
Local helper function to check that n and k are valid for a binomial coefficient.
Definition at line 427 of file binomial.cpp.
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.
|
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.
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.
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.
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.
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.
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.
|
static |
|
constexprnoexcept |
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
).
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.
|
static |
|
static |
Definition at line 157 of file strict_fstream.cpp.
|
static |
Definition at line 177 of file strict_fstream.cpp.
|
static |
Definition at line 188 of file strict_fstream.cpp.
|
inline |
Definition at line 57 of file common.hpp.
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.
|
inline |
Calculate the closure of a std::vector
of double
elements.
Definition at line 330 of file statistics.hpp.
|
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.
|
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 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 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 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().
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.
Color color_from_name_web | ( | std::string const & | name | ) |
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.
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.
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.
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.
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.
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.
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.
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.
std::vector< Color > const & color_list_diverging | ( | ColorListDiverging | palette | ) |
Definition at line 249 of file list_diverging.cpp.
std::vector< Color > const & color_list_diverging | ( | std::string const & | palette | ) |
Definition at line 282 of file list_diverging.cpp.
std::vector< std::string > color_list_diverging_names | ( | ) |
Definition at line 317 of file list_diverging.cpp.
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.
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.
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.
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.
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.
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.
std::vector< Color > const & color_list_misc | ( | ColorListMisc | palette | ) |
Definition at line 480 of file list_misc.cpp.
std::vector< Color > const & color_list_misc | ( | std::string const & | palette | ) |
Definition at line 489 of file list_misc.cpp.
std::vector< std::string > color_list_misc_names | ( | ) |
Definition at line 500 of file list_misc.cpp.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
std::vector< Color > const & color_list_qualitative | ( | ColorListQualitative | palette | ) |
Definition at line 202 of file list_qualitative.cpp.
std::vector< Color > const & color_list_qualitative | ( | std::string const & | palette | ) |
Definition at line 232 of file list_qualitative.cpp.
std::vector< std::string > color_list_qualitative_names | ( | ) |
Definition at line 264 of file list_qualitative.cpp.
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.
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.
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.
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.
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.
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.
std::vector< Color > const & color_list_sequential | ( | ColorListSequential | palette | ) |
Definition at line 1530 of file list_sequential.cpp.
std::vector< Color > const & color_list_sequential | ( | std::string const & | palette | ) |
Definition at line 1608 of file list_sequential.cpp.
std::vector< std::string > color_list_sequential_names | ( | ) |
Definition at line 1688 of file list_sequential.cpp.
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.
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.
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.
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.
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.
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.
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.
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.
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.
std::map< double, Color > color_stops | ( | ColorMap const & | map, |
ColorNormalization const & | norm | ||
) |
Definition at line 53 of file helpers.cpp.
std::map< double, Color > color_stops | ( | ColorMap const & | map, |
ColorNormalizationBoundary const & | norm | ||
) |
Definition at line 138 of file helpers.cpp.
std::map< double, Color > color_stops | ( | ColorMap const & | map, |
ColorNormalizationDiverging const & | norm | ||
) |
Definition at line 94 of file helpers.cpp.
std::map< double, Color > color_stops | ( | ColorMap const & | map, |
ColorNormalizationLinear const & | norm | ||
) |
Definition at line 78 of file helpers.cpp.
std::map< double, Color > color_stops | ( | ColorMap const & | map, |
ColorNormalizationLogarithmic const & | norm | ||
) |
Definition at line 89 of file helpers.cpp.
std::map< double, std::string > color_tickmarks | ( | ColorNormalization const & | norm, |
size_t | num_ticks | ||
) |
Definition at line 157 of file helpers.cpp.
std::map< double, std::string > color_tickmarks | ( | ColorNormalizationBoundary const & | norm, |
size_t | num_ticks | ||
) |
Definition at line 262 of file helpers.cpp.
std::map< double, std::string > color_tickmarks | ( | ColorNormalizationDiverging const & | norm, |
size_t | num_ticks | ||
) |
Definition at line 215 of file helpers.cpp.
std::map< double, std::string > color_tickmarks | ( | ColorNormalizationLinear const & | norm, |
size_t | num_ticks | ||
) |
Definition at line 182 of file helpers.cpp.
std::map< double, std::string > color_tickmarks | ( | ColorNormalizationLogarithmic const & | norm, |
size_t | num_ticks | ||
) |
Definition at line 193 of file helpers.cpp.
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.
|
inlineconstexpr |
|
inlineconstexpr |
|
inlineconstexpr |
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.
|
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.
|
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.
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.
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.
|
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.
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.
|
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.
|
inline |
Specialization of the generic conversion function for std::string
.
Definition at line 89 of file convert.hpp.
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.
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.
|
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.
void convert_to_bool | ( | Dataframe & | df, |
size_t | col_index | ||
) |
Definition at line 156 of file utils/containers/dataframe/operators.cpp.
void convert_to_bool | ( | Dataframe & | df, |
std::string const & | col_name | ||
) |
Definition at line 186 of file utils/containers/dataframe/operators.cpp.
std::vector<bool> genesis::utils::convert_to_bool | ( | ForwardIterator | first, |
ForwardIterator | last, | ||
size_t | size = 0 |
||
) |
Definition at line 144 of file convert.hpp.
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.
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.
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.
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.
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.
void convert_to_double | ( | Dataframe & | df, |
size_t | col_index | ||
) |
Definition at line 192 of file utils/containers/dataframe/operators.cpp.
void convert_to_double | ( | Dataframe & | df, |
std::string const & | col_name | ||
) |
Definition at line 206 of file utils/containers/dataframe/operators.cpp.
std::vector<double> genesis::utils::convert_to_double | ( | ForwardIterator | first, |
ForwardIterator | last, | ||
size_t | size = 0 |
||
) |
Definition at line 260 of file convert.hpp.
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.
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.
bool genesis::utils::convert_to_numeric_ | ( | std::string const & | str, |
T & | result, | ||
T | initial, | ||
F | conversion | ||
) |
Definition at line 123 of file convert.cpp.
|
static |
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
void genesis::utils::convert_to_type_ | ( | Dataframe & | df, |
size_t | col_index | ||
) |
Definition at line 111 of file utils/containers/dataframe/operators.cpp.
void genesis::utils::convert_to_type_ | ( | Dataframe & | df, |
size_t | col_index | ||
) |
Definition at line 123 of file utils/containers/dataframe/operators.cpp.
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.
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.
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.
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.
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.
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.
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.
|
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.
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.
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.
|
static |
|
static |
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.
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.
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.
|
inline |
Sort two values in descending order, inplace.
Definition at line 81 of file common.hpp.
void dir_create | ( | std::string const & | path, |
bool | with_parents = true |
||
) |
bool dir_exists | ( | std::string const & | dir | ) |
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
.
|
static |
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.
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.
std::string dir_normalize_path | ( | std::string const & | path | ) |
TableLayout double_frame | ( | bool | condensed | ) |
Definition at line 573 of file utils/text/table.cpp.
TableLayout double_grid | ( | bool | condensed | ) |
Definition at line 554 of file utils/text/table.cpp.
Definition at line 48 of file utils/math/histogram/distances.cpp.
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.
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.
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.
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.
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.
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.
Definition at line 55 of file histogram.cpp.
bool equals_ci | ( | std::string const & | lhs, |
std::string const & | rhs | ||
) |
Compare two strings, case insensitive.
Definition at line 114 of file string.cpp.
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.
|
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.
c | The container to modify. |
p | The predicate to satisfy. |
Definition at line 107 of file algorithm.hpp.
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.
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.
|
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.
Matrix< double > eucl |