This class provides some common tools for developping applications. More...

#include <Bpp/App/ApplicationTools.h>

Collaboration diagram for bpp::ApplicationTools:

Public Member Functions
	ApplicationTools ()

virtual	~ApplicationTools ()

Static Public Member Functions
static bool	parameterExists (const std::string &parameterName, std::map< std::string, std::string > &params)
	Tells if a parameter have been specified. More...

static bool	parameterExists (const std::string &parameterName, std::vector< std::string > &params)

static std::vector< std::string >	matchingParameters (const std::string &pattern, std::map< std::string, std::string > &params)
	Returns a vector of parameter names that match a given pattern. More...

static std::vector< std::string >	matchingParameters (const std::string &pattern, std::vector< std::string > &params)

static double	getDoubleParameter (const std::string &parameterName, std::map< std::string, std::string > &params, double defaultValue, const std::string &suffix="", bool suffixIsOptional=true, int warn=0)
	Get a double parameter. More...

static int	getIntParameter (const std::string &parameterName, std::map< std::string, std::string > &params, int defaultValue, const std::string &suffix="", bool suffixIsOptional=true, int warn=0)
	Get an integer parameter. More...

static std::string	getStringParameter (const std::string &parameterName, std::map< std::string, std::string > &params, const std::string &defaultValue, const std::string &suffix="", bool suffixIsOptional=true, int warn=0)
	Get a string parameter. More...

static bool	getBooleanParameter (const std::string &parameterName, std::map< std::string, std::string > &params, bool defaultValue, const std::string &suffix="", bool suffixIsOptional=true, int warn=0)
	Get a boolean parameter. More...

template<class T >
static T	getParameter (const std::string &parameterName, std::map< std::string, std::string > &params, T defaultValue, const std::string &suffix="", bool suffixIsOptional=true, int warn=0)
	Get a parameter. More...

static std::string	getAFilePath (const std::string &parameter, std::map< std::string, std::string > &params, bool isRequired=true, bool mustExist=true, const std::string &suffix="", bool suffixIsOptional=false, const std::string &defaultPath="none", int warn=0) throw (Exception)
	Get a file path. More...

template<class T >
static std::vector< T >	getVectorParameter (const std::string &parameterName, std::map< std::string, std::string > &params, char separator, const std::string &defaultValue, const std::string &suffix="", bool suffixIsOptional=true, int warn=0)
	Get a vector. More...

template<class T >
static std::vector< T >	getVectorParameter (const std::string &parameterName, std::map< std::string, std::string > &params, char separator, char rangeOperator, const std::string &defaultValue, const std::string &suffix="", bool suffixIsOptional=true, bool warn=true)
	Get a vector. More...

template<class T >
static RowMatrix< T >	getMatrixParameter (const std::string &parameterName, std::map< std::string, std::string > &params, char separator, const std::string &defaultValue, const std::string &suffix="", bool suffixIsOptional=true, bool warn=true)
	Get a RowMatrix. The input is made of embedded parenthesis, such as ((1,2),(3,4)), where the matrix is filled by lines. Here, the matrix would be: $\begin{pmatrix} 1 & 2 \\ 3 & 4 \\ \end{pmatrix}$ . More...

static void	startTimer ()
	Starts the timer. More...

static void	displayTime (const std::string &msg)
	Display the current timer value to the 'message' stream. More...

static double	getTime ()
	Get the current timer value. More...

Output methods.
static void	displayMessage (const std::string &text)
	Print a message. More...

static void	displayError (const std::string &text)
	Print an error message. More...

static void	displayWarning (const std::string &text)
	Print a warning message. More...

static void	displayTask (const std::string &text, bool eof=false)
	Print a task message. More...

static void	displayTaskDone ()
	Print a task ended message. More...

template<class T >
static void	displayResult (const std::string &text, const T &result)
	Print a result message. More...

static void	displayBooleanResult (const std::string &text, bool result)
	Print a boolean result message ("yes" or "no"). More...

static void	displayGauge (size_t iter, size_t total, char symbol='>', const std::string &mes="")
	Display a gauge. More...

static void	displayUnlimitedGauge (size_t iter, const std::string &mes="")
	Display a gauge for unefined amount of iterations. More...

Static Public Attributes
static OutputStream *	error = new StdErr()
	The output stream where errors have to be displayed. More...

static OutputStream *	message = new StdOut()
	The output stream where messages have to be displayed. More...

static OutputStream *	warning = new StdOut()
	The output stream where warnings have to be displayed. More...

static time_t	startTime
	Timer variable. More...

static size_t	terminalWidth = 80
	The width of the output terminal (in character). More...

static float	terminalSplit = 0.5
	The fraction of terminal width dedicated to messages. More...

static bool	interactive = true
	Tell if the program is interactive (typically run in foreground). Default to yes. More...

static int	warningLevel = 0
	Specify the amount of warning to display. More...

Detailed Description

This class provides some common tools for developping applications.

These functions are designed for helping to parse an option file.

The option files are supposed to follow this simple format:

parameterName = parameterContent

with one parameter per line.

In files, shell comments:

# my comment line here

C comments:

/ * my comment block here * /

and C++ comments:

// my comment line here

are allowed, and ignored while parsing.

Some methods for displaying information (messages, errors, warnings...) are also provided.

Methods dealing with parameters takes as argument a map<string, string> object containing the parameters (names are the keys of the map, and values are... the values of the map!). These map objects may be obtained from the AttributesTools utilitary class.

Definition at line 92 of file ApplicationTools.h.

Constructor & Destructor Documentation

◆ ApplicationTools()

bpp::ApplicationTools::ApplicationTools ( )

inline

Definition at line 135 of file ApplicationTools.h.

◆ ~ApplicationTools()

virtual bpp::ApplicationTools::~ApplicationTools ( )

inlinevirtual

Definition at line 136 of file ApplicationTools.h.

Member Function Documentation

◆ displayBooleanResult()

static void bpp::ApplicationTools::displayBooleanResult	(	const std::string &	text,
		bool	result
	)

inlinestatic

Print a boolean result message ("yes" or "no").

Result will be aligned to 30 character from the begining of the message.

Parameters

text	The text of the message.
result	The result.

Definition at line 524 of file ApplicationTools.h.

References displayResult().

◆ displayError()

void ApplicationTools::displayError ( const std::string & text )

static

Print an error message.

Parameters

text	The text of the message.

Definition at line 302 of file ApplicationTools.cpp.

◆ displayGauge()

void ApplicationTools::displayGauge	(	size_t	iter,
		size_t	total,
		char	symbol = `'>'`,
		const std::string &	mes = `""`
	)

static

Display a gauge.

Show progress status.

for(size_t i = 0; i < 1000; i++)
{
  ApplicationTools::displayGauge(i, 999, '*');
  //Perform time consuming task...
}

will result in something like:

* [************************************]
*

Parameters

iter	The current iteration number.
total	The total number of iteration.
symbol	The character to display in the gauge.
mes	A message to print before the gauge.

Definition at line 320 of file ApplicationTools.cpp.

References bpp::TextTools::resizeLeft(), bpp::TextTools::resizeRight(), and bpp::TextTools::toString().

Referenced by bpp::FunctionTools::computeGrid().

◆ displayMessage()

void ApplicationTools::displayMessage ( const std::string & text )

static

Print a message.

Parameters

text	The text of the message.

Definition at line 300 of file ApplicationTools.cpp.

Referenced by bpp::FunctionTools::computeGrid(), displayResult(), and bpp::ReparametrizationFunctionWrapper::init_().

◆ displayResult()

template<class T >

static void bpp::ApplicationTools::displayResult	(	const std::string &	text,
		const T &	result
	)

inlinestatic

Print a result message.

Result will be aligned to 30 character from the begining of the message. ex: text = "Here is what you get:" and result = "THAT" gives "Here is what you get: THAT".

Parameters

text	The text of the message.
result	The result.

Definition at line 512 of file ApplicationTools.h.

References displayMessage(), bpp::TextTools::resizeRight(), terminalSplit, and terminalWidth.

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::BppApplication::BppApplication(), displayBooleanResult(), bpp::BppODiscreteDistributionFormat::initialize_(), and bpp::BppODiscreteDistributionFormat::read().

◆ displayTask()

void ApplicationTools::displayTask	(	const std::string &	text,
		bool	eof = `false`
	)

static

Print a task message.

Display the message and flush the buffer, but do not end the current line.

Parameters

text	The text of the message.
eof	Insert a carriage return after displaying the message.

Definition at line 306 of file ApplicationTools.cpp.

◆ displayTaskDone()

void ApplicationTools::displayTaskDone ( )

static

Print a task ended message.

Print "Done." and go to next line.

Definition at line 316 of file ApplicationTools.cpp.

◆ displayTime()

void ApplicationTools::displayTime ( const std::string & msg )

static

Display the current timer value to the 'message' stream.

Parameters

msg	Message to display before time.

Definition at line 381 of file ApplicationTools.cpp.

Referenced by bpp::BppApplication::done().

◆ displayUnlimitedGauge()

void ApplicationTools::displayUnlimitedGauge	(	size_t	iter,
		const std::string &	mes = `""`
	)

static

Display a gauge for unefined amount of iterations.

Show progress status.

for(size_t i = 0; i < 1000; i++)
{
  ApplicationTools::displayUnlimitedGauge(i);
  //Perform time consuming task...
}

will result in something like:

* - 1
* / 2
* - 3
* \ 4
* - 5
* etc
*

Parameters

iter	The current iteration number.
mes	A message to print before the gauge.

Definition at line 358 of file ApplicationTools.cpp.

References bpp::TextTools::toString().

Referenced by bpp::AbstractOptimizer::optimize().

◆ displayWarning()

void ApplicationTools::displayWarning ( const std::string & text )

static

Print a warning message.

Parameters

text	The text of the message.

Definition at line 304 of file ApplicationTools.cpp.

Referenced by bpp::DualityDiagram::compute_(), bpp::ContingencyTableTest::ContingencyTableTest(), getParameter(), and bpp::ReparametrizationFunctionWrapper::init_().

◆ getAFilePath()

string ApplicationTools::getAFilePath	(	const std::string &	parameter,
		std::map< std::string, std::string > &	params,
		bool	isRequired = `true`,
		bool	mustExist = `true`,
		const std::string &	suffix = `""`,
		bool	suffixIsOptional = `false`,
		const std::string &	defaultPath = `"none"`,
		int	warn = `0`
	)
throw	(	Exception
	)

static

Get a file path.

Parameters

parameter	The name of the corresponding parameter.
params	The attribute map where options may be found.
isRequired	Tell if this path is strictly required or is optional (in the first case, if the parameter is not found, the programm will send an error and exit).
mustExist	Tell if the corresponding file must already exist.
suffix	A suffix to be applied to the parameter name.
suffixIsOptional	Tell if the suffix is absolutely required.
defaultPath	Path to use if no argument is provided.
warn	Tell if a warning must be sent in case the parameter is not found.

Exceptions

Exception If no file path is specified and isRequired is true, or the file does not exist and mustExist is set to true.

Definition at line 154 of file ApplicationTools.cpp.

References bpp::FileTools::fileExists().

◆ getBooleanParameter()

bool ApplicationTools::getBooleanParameter	(	const std::string &	parameterName,
		std::map< std::string, std::string > &	params,
		bool	defaultValue,
		const std::string &	suffix = `""`,
		bool	suffixIsOptional = `true`,
		int	warn = `0`
	)

static

Get a boolean parameter.

Parameters

parameterName	The name of the corresponding parameter.
params	The attribute map where options may be found.
defaultValue	The default value to use if the parameter is not found.
suffix	A suffix to be applied to the parameter name.
suffixIsOptional	Tell if the suffix is absolutely required.
warn	Tell if a warning must be sent in case the parameter is not found.

Returns: The corresponding value.

Definition at line 248 of file ApplicationTools.cpp.

References bpp::TextTools::toString().

Referenced by bpp::BppApplication::BppApplication().

◆ getDoubleParameter()

double ApplicationTools::getDoubleParameter	(	const std::string &	parameterName,
		std::map< std::string, std::string > &	params,
		double	defaultValue,
		const std::string &	suffix = `""`,
		bool	suffixIsOptional = `true`,
		int	warn = `0`
	)

static

Get a double parameter.

Parameters

parameterName	The name of the corresponding parameter.
params	The attribute map where options may be found.
defaultValue	The default value to use if the parameter is not found.
suffix	A suffix to be applied to the parameter name.
suffixIsOptional	Tell if the suffix is absolutely required.
warn	Tell if a warning must be sent in case the parameter is not found.

Returns: The corresponding value.

Definition at line 180 of file ApplicationTools.cpp.

References bpp::TextTools::toDouble(), and bpp::TextTools::toString().

Referenced by bpp::BppODiscreteDistributionFormat::initialize_().

◆ getIntParameter()

int ApplicationTools::getIntParameter	(	const std::string &	parameterName,
		std::map< std::string, std::string > &	params,
		int	defaultValue,
		const std::string &	suffix = `""`,
		bool	suffixIsOptional = `true`,
		int	warn = `0`
	)

static

Get an integer parameter.

Parameters

parameterName	The name of the corresponding parameter.
params	The attribute map where options may be found.
defaultValue	The default value to use if the parameter is not found.
suffix	A suffix to be applied to the parameter name.
suffixIsOptional	Tell if the suffix is absolutely required.
warn	Tell if a warning must be sent in case the parameter is not found.

Returns: The corresponding value.

Definition at line 206 of file ApplicationTools.cpp.

References bpp::TextTools::toInt(), and bpp::TextTools::toString().

Referenced by bpp::BppApplication::BppApplication().

◆ getMatrixParameter()

template<class T >

static RowMatrix<T> bpp::ApplicationTools::getMatrixParameter	(	const std::string &	parameterName,
		std::map< std::string, std::string > &	params,
		char	separator,
		const std::string &	defaultValue,
		const std::string &	suffix = `""`,
		bool	suffixIsOptional = `true`,
		bool	warn = `true`
	)

inlinestatic

Get a RowMatrix. The input is made of embedded parenthesis, such as ((1,2),(3,4)), where the matrix is filled by lines. Here, the matrix would be:

$\begin{pmatrix} 1 & 2 \\ 3 & 4 \\ \end{pmatrix}$

.

Parameters

parameterName	The name of the corresponding parameter.
params	The attribute map where options may be found.
separator	The character used to delimit values.
defaultValue	The default value to use if the parameter is not found.
suffix	A suffix to be applied to the parameter name.
suffixIsOptional	Tell if the suffix is absolutely required.
warn	Tell if a warning must be sent in case the parameter is not found.

Returns: The corresponding value.

Definition at line 417 of file ApplicationTools.h.

References bpp::RowMatrix< Scalar >::addRow(), getStringParameter(), bpp::StringTokenizer::hasMoreToken(), bpp::TextTools::isEmpty(), bpp::StringTokenizer::nextToken(), bpp::StringTokenizer::numberOfRemainingTokens(), and bpp::TextTools::toString().

◆ getParameter()

template<class T >

static T bpp::ApplicationTools::getParameter	(	const std::string &	parameterName,
		std::map< std::string, std::string > &	params,
		T	defaultValue,
		const std::string &	suffix = `""`,
		bool	suffixIsOptional = `true`,
		int	warn = `0`
	)

inlinestatic

Get a parameter.

Parameters

parameterName	The name of the corresponding parameter.
params	The attribute map where options may be found.
defaultValue	The default value to use if the parameter is not found.
suffix	A suffix to be applied to the parameter name.
suffixIsOptional	Tell if the suffix is absolutely required.
warn	Tell if a warning must be sent in case the parameter is not found.

Returns: The corresponding value.

Definition at line 251 of file ApplicationTools.h.

References displayWarning(), parameterExists(), bpp::TextTools::toString(), and warningLevel.

◆ getStringParameter()

std::string ApplicationTools::getStringParameter	(	const std::string &	parameterName,
		std::map< std::string, std::string > &	params,
		const std::string &	defaultValue,
		const std::string &	suffix = `""`,
		bool	suffixIsOptional = `true`,
		int	warn = `0`
	)

static

Get a string parameter.

Parameters

parameterName	The name of the corresponding parameter.
params	The attribute map where options may be found.
defaultValue	The default value to use if the parameter is not found.
suffix	A suffix to be applied to the parameter name.
suffixIsOptional	Tell if the suffix is absolutely required.
warn	Tell if a warning must be sent in case the parameter is not found.

Returns: The corresponding value.

Definition at line 227 of file ApplicationTools.cpp.

Referenced by getMatrixParameter(), bpp::NumCalcApplicationTools::getParameterGrid(), and getVectorParameter().

◆ getTime()

double ApplicationTools::getTime ( )

static

Get the current timer value.

Returns: The number of seconds from when timer was started.

Definition at line 405 of file ApplicationTools.cpp.

◆ getVectorParameter() [1/2]

template<class T >

static std::vector<T> bpp::ApplicationTools::getVectorParameter	(	const std::string &	parameterName,
		std::map< std::string, std::string > &	params,
		char	separator,
		const std::string &	defaultValue,
		const std::string &	suffix = `""`,
		bool	suffixIsOptional = `true`,
		int	warn = `0`
	)

inlinestatic

Get a vector.

Parameters

parameterName	The name of the corresponding parameter.
params	The attribute map where options may be found.
separator	The character used to delimit values.
defaultValue	The default value to use if the parameter is not found.
suffix	A suffix to be applied to the parameter name.
suffixIsOptional	Tell if the suffix is absolutely required.
warn	Tell if a warning must be sent in case the parameter is not found.

Returns: The corresponding value.

Definition at line 315 of file ApplicationTools.h.

References getStringParameter(), bpp::TextTools::isEmpty(), bpp::NestedStringTokenizer::nextToken(), bpp::StringTokenizer::numberOfRemainingTokens(), and bpp::TextTools::toString().

◆ getVectorParameter() [2/2]

template<class T >

static std::vector<T> bpp::ApplicationTools::getVectorParameter	(	const std::string &	parameterName,
		std::map< std::string, std::string > &	params,
		char	separator,
		char	rangeOperator,
		const std::string &	defaultValue,
		const std::string &	suffix = `""`,
		bool	suffixIsOptional = `true`,
		bool	warn = `true`
	)

inlinestatic

Get a vector.

Similar to getVectorParameter, but dedicated to numerical values. It allows the possibility to set range of values, which will be incremented by 1 (like the : operator in R).

Parameters

parameterName	The name of the corresponding parameter.
params	The attribute map where options may be found.
separator	The character used to delimit values.
rangeOperator	The character used to delimit ranges (the + 1 operator must be available for T).
defaultValue	The default value to use if the parameter is not found.
suffix	A suffix to be applied to the parameter name.
suffixIsOptional	Tell if the suffix is absolutely required.
warn	Tell if a warning must be sent in case the parameter is not found.

Returns: The corresponding value.

Definition at line 357 of file ApplicationTools.h.

References getStringParameter(), bpp::TextTools::isEmpty(), bpp::StringTokenizer::nextToken(), bpp::StringTokenizer::numberOfRemainingTokens(), and bpp::TextTools::toString().

◆ matchingParameters() [1/2]

std::vector< std::string > ApplicationTools::matchingParameters	(	const std::string &	pattern,
		std::map< std::string, std::string > &	params
	)

static

Returns a vector of parameter names that match a given pattern.

Only "*" wildcard is implemented now.

Parameters

pattern	The pattern.
params	The parameter list.

Returns: a vector of matching names.

Definition at line 83 of file ApplicationTools.cpp.

References bpp::StringTokenizer::hasMoreToken(), and bpp::StringTokenizer::nextToken().

◆ matchingParameters() [2/2]

std::vector< std::string > ApplicationTools::matchingParameters	(	const std::string &	pattern,
		std::vector< std::string > &	params
	)

static

Definition at line 118 of file ApplicationTools.cpp.

References bpp::StringTokenizer::hasMoreToken(), and bpp::StringTokenizer::nextToken().

◆ parameterExists() [1/2]

bool ApplicationTools::parameterExists	(	const std::string &	parameterName,
		std::map< std::string, std::string > &	params
	)

static

Tells if a parameter have been specified.

Parameters

parameterName	The name of the parameter.
params	The parameter list.

Returns: True is the parameter of specified name is in the list.

Definition at line 63 of file ApplicationTools.cpp.

References bpp::TextTools::isEmpty().

Referenced by getParameter().

◆ parameterExists() [2/2]

bool ApplicationTools::parameterExists	(	const std::string &	parameterName,
		std::vector< std::string > &	params
	)

static

Definition at line 70 of file ApplicationTools.cpp.

◆ startTimer()

static void bpp::ApplicationTools::startTimer ( )

inlinestatic

Starts the timer.

Definition at line 584 of file ApplicationTools.h.

References startTime.

Referenced by bpp::BppApplication::startTimer().

Member Data Documentation

◆ error

OutputStream * ApplicationTools::error = new StdErr()

static

The output stream where errors have to be displayed.

Definition at line 99 of file ApplicationTools.h.

Referenced by bpp::ReparametrizationFunctionWrapper::fireParameterChanged().

◆ interactive

bool ApplicationTools::interactive = true

static

Tell if the program is interactive (typically run in foreground). Default to yes.

Definition at line 127 of file ApplicationTools.h.

Referenced by bpp::BppApplication::BppApplication().

◆ message

OutputStream * ApplicationTools::message = new StdOut()

static

The output stream where messages have to be displayed.

Definition at line 103 of file ApplicationTools.h.

Referenced by bpp::MetaOptimizer::doStep().

◆ startTime

time_t ApplicationTools::startTime

static

Timer variable.

Definition at line 112 of file ApplicationTools.h.

Referenced by startTimer().

◆ terminalSplit

float ApplicationTools::terminalSplit = 0.5

static

The fraction of terminal width dedicated to messages.

Definition at line 122 of file ApplicationTools.h.

Referenced by displayResult().

◆ terminalWidth

size_t ApplicationTools::terminalWidth = 80

static

The width of the output terminal (in character).

Definition at line 117 of file ApplicationTools.h.

Referenced by displayResult().

◆ warning

OutputStream * ApplicationTools::warning = new StdOut()

static

The output stream where warnings have to be displayed.

Definition at line 107 of file ApplicationTools.h.

Referenced by bpp::RescaledHmmLikelihood::computeForward_(), and bpp::BppODiscreteDistributionFormat::initialize_().

◆ warningLevel

int ApplicationTools::warningLevel = 0

static

Specify the amount of warning to display.

Definition at line 132 of file ApplicationTools.h.

Referenced by bpp::BppApplication::BppApplication(), and getParameter().

The documentation for this class was generated from the following files:

Bpp/App/ApplicationTools.h
Bpp/App/ApplicationTools.cpp

Public Member Functions

Static Public Member Functions

Static Public Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ApplicationTools()

◆ ~ApplicationTools()

Member Function Documentation

◆ displayBooleanResult()

◆ displayError()

◆ displayGauge()

◆ displayMessage()

◆ displayResult()

◆ displayTask()

◆ displayTaskDone()

◆ displayTime()

◆ displayUnlimitedGauge()

◆ displayWarning()

◆ getAFilePath()

◆ getBooleanParameter()

◆ getDoubleParameter()

◆ getIntParameter()

◆ getMatrixParameter()

◆ getParameter()

◆ getStringParameter()

◆ getTime()

◆ getVectorParameter() [1/2]

◆ getVectorParameter() [2/2]

◆ matchingParameters() [1/2]

◆ matchingParameters() [2/2]

◆ parameterExists() [1/2]

◆ parameterExists() [2/2]

◆ startTimer()

Member Data Documentation

◆ error

◆ interactive

◆ message

◆ startTime

◆ terminalSplit

◆ terminalWidth

◆ warning

◆ warningLevel