bpp::ApplicationTools Class Reference

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

#include <Bpp/App/ApplicationTools.h>

Collaboration diagram for bpp::ApplicationTools:

List of all members.

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.
static double	getDoubleParameter (const std::string &parameterName, std::map< std::string, std::string > &params, double defaultValue, const std::string &suffix="", bool suffixIsOptional=true, bool warn=true)
	Get a double parameter.
static int	getIntParameter (const std::string &parameterName, std::map< std::string, std::string > &params, int defaultValue, const std::string &suffix="", bool suffixIsOptional=true, bool warn=true)
	Get an integer parameter.
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, bool warn=true)
	Get a string parameter.
static bool	getBooleanParameter (const std::string &parameterName, std::map< std::string, std::string > &params, bool defaultValue, const std::string &suffix="", bool suffixIsOptional=true, bool warn=true)
	Get a boolean parameter.
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, bool warn=true)
	Get a parameter.
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) throw (Exception)
	Get a file path.
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, bool warn=true)
	Get a vector.
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.
static void	startTimer ()
	Starts the timer.
static void	displayTime (const std::string &msg)
	Display the current timer value to the 'message' stream.
static double	getTime ()
	Get the current timer value.
Output methods.
static void	displayMessage (const std::string &text)
	Print a message.
static void	displayError (const std::string &text)
	Print an error message.
static void	displayWarning (const std::string &text)
	Print a warning message.
static void	displayTask (const std::string &text, bool eof=false)
	Print a task message.
static void	displayTaskDone ()
	Print a task ended message.
template<class T >
static void	displayResult (const std::string &text, const T &result)
	Print a result message.
static void	displayBooleanResult (const std::string &text, bool result)
	Print a boolean result message ("yes" or "no").
static void	displayGauge (size_t iter, size_t total, char symbol='>', const std::string &mes="")
	Display a gauge.
static void	displayUnlimitedGauge (size_t iter, const std::string &mes="")
	Display a gauge for unefined amount of iterations.
Static Public Attributes
static OutputStream *	error = new StdErr()
	The output stream where errors have to be displayed.
static OutputStream *	message = new StdOut()
	The output stream where messages have to be displayed.
static OutputStream *	warning = new StdOut()
	The output stream where warnings have to be displayed.
static time_t	startTime
	Timer variable.
static size_t	terminalWidth = 80
	The width of the output terminal (in character).
static float	terminalSplit = 0.5
	The fraction of terminal width dedicated to messages.
static bool	interactive = true
	Tell if the program is interactive (typically run in foreground). Default to yes.

---

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 90 of file ApplicationTools.h.

---

Constructor & Destructor Documentation

bpp::ApplicationTools::ApplicationTools

(

)

[inline]

Definition at line 128 of file ApplicationTools.h.

virtual bpp::ApplicationTools::~ApplicationTools

(

)

[inline, virtual]

Definition at line 129 of file ApplicationTools.h.

---

Member Function Documentation

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

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 431 of file ApplicationTools.h.

References displayResult().

void ApplicationTools::displayError

(

const std::string &

text

)

[static]

Print an error message.

Parameters:

text	The text of the message.

Definition at line 217 of file ApplicationTools.cpp.

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 235 of file ApplicationTools.cpp.

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

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

void ApplicationTools::displayMessage

(

const std::string &

text

)

[static]

Print a message.

Parameters:

text	The text of the message.

Definition at line 215 of file ApplicationTools.cpp.

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

template<class T >

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

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 419 of file ApplicationTools.h.

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

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

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 221 of file ApplicationTools.cpp.

void ApplicationTools::displayTaskDone

(

)

[static]

Print a task ended message.

Print "Done." and go to next line.

Definition at line 231 of file ApplicationTools.cpp.

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 297 of file ApplicationTools.cpp.

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

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 274 of file ApplicationTools.cpp.

References bpp::TextTools::toString().

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

void ApplicationTools::displayWarning

(

const std::string &

text

)

[static]

Print a warning message.

Parameters:

text	The text of the message.

Definition at line 219 of file ApplicationTools.cpp.

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

std::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
	)		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.

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 71 of file ApplicationTools.cpp.

References bpp::FileTools::fileExists().

bool ApplicationTools::getBooleanParameter	(	const std::string &	parameterName,
		std::map< std::string, std::string > &	params,
		bool	defaultValue,
		const std::string &	suffix = "",
		bool	suffixIsOptional = true,
		bool	warn = true
	)		[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 163 of file ApplicationTools.cpp.

References bpp::TextTools::toString().

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

double ApplicationTools::getDoubleParameter	(	const std::string &	parameterName,
		std::map< std::string, std::string > &	params,
		double	defaultValue,
		const std::string &	suffix = "",
		bool	suffixIsOptional = true,
		bool	warn = true
	)		[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 95 of file ApplicationTools.cpp.

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

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

int ApplicationTools::getIntParameter	(	const std::string &	parameterName,
		std::map< std::string, std::string > &	params,
		int	defaultValue,
		const std::string &	suffix = "",
		bool	suffixIsOptional = true,
		bool	warn = true
	)		[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 121 of file ApplicationTools.cpp.

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

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,
		bool	warn = true
	)		[inline, static]

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 229 of file ApplicationTools.h.

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

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,
		bool	warn = true
	)		[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 142 of file ApplicationTools.cpp.

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

double ApplicationTools::getTime

(

)

[static]

Get the current timer value.

Returns:

The number of seconds from when timer was started.

Definition at line 321 of file ApplicationTools.cpp.

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,
		bool	warn = true
	)		[inline, static]

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 288 of file ApplicationTools.h.

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

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
	)		[inline, static]

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 330 of file ApplicationTools.h.

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

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 62 of file ApplicationTools.cpp.

References bpp::TextTools::isEmpty().

Referenced by getParameter().

static void bpp::ApplicationTools::startTimer

(

)

[inline, static]

Starts the timer.

Definition at line 491 of file ApplicationTools.h.

References startTime.

---

Member Data Documentation

OutputStream * ApplicationTools::error = new StdErr() [static]

The output stream where errors have to be displayed.

Definition at line 97 of file ApplicationTools.h.

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

bool ApplicationTools::interactive = true [static]

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

Definition at line 125 of file ApplicationTools.h.

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

OutputStream * ApplicationTools::message = new StdOut() [static]

The output stream where messages have to be displayed.

Definition at line 101 of file ApplicationTools.h.

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

time_t ApplicationTools::startTime [static]

Timer variable.

Definition at line 110 of file ApplicationTools.h.

Referenced by startTimer().

float ApplicationTools::terminalSplit = 0.5 [static]

The fraction of terminal width dedicated to messages.

Definition at line 120 of file ApplicationTools.h.

Referenced by displayResult().

size_t ApplicationTools::terminalWidth = 80 [static]

The width of the output terminal (in character).

Definition at line 115 of file ApplicationTools.h.

Referenced by displayResult().

OutputStream * ApplicationTools::warning = new StdOut() [static]

The output stream where warnings have to be displayed.

Definition at line 105 of file ApplicationTools.h.

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

---

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

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