Algorithm Class Reference

Framework class for implementing algorithm. More...

#include <Algorithm.hpp>

Inheritance diagram for Algorithm:

Public Member Functions
	Algorithm (const std::string &name, int nbCores=-1, gatb::core::tools::misc::IProperties *input=0)
virtual	~Algorithm ()
std::string	getName () const
void	run ()
virtual void	execute ()=0
virtual IProperties *	getInput ()
virtual IProperties *	getOutput ()
virtual IProperties *	getInfo ()
virtual dp::IDispatcher *	getDispatcher ()
virtual TimeInfo &	getTimeInfo ()
virtual IProperties *	getSystemInfo ()
template<typename Item >
dp::Iterator< Item > *	createIterator (dp::Iterator< Item > *iter, size_t nbIterations=0, const char *message=0, dp::IteratorListener *listener=0)
virtual dp::IteratorListener *	createIteratorListener (size_t nbIterations, const char *message)
Public Member Functions inherited from SmartPointer
void	use ()
void	forget ()
Public Member Functions inherited from ISmartPointer
virtual	~ISmartPointer ()

Static Public Member Functions
template<template< size_t > class Functor>
static int	mainloop (tools::misc::IOptionsParser *parser, int argc, char *argv[])

Protected Member Functions
std::string	getUriByKey (const std::string &key)
std::string	getUri (const std::string &str)
void	setInput (IProperties *input)
Protected Member Functions inherited from SmartPointer
	SmartPointer ()
virtual	~SmartPointer ()

Detailed Description

Framework class for implementing algorithm.

See also

Tool

Constructor & Destructor Documentation

Algorithm	(	const std::string &	name,
		int	nbCores = -1,
		gatb::core::tools::misc::IProperties *	input = 0
	)

Constructor.

Parameters

[in]	name	name of the algorithm.
[in]	nbCores	: number of cores to be used for this algorithm.
[in]	input	: extra options for configuring the algorithm.

~Algorithm ( )

virtual

Destructor.

Member Function Documentation

dp::Iterator<Item>* createIterator ( dp::Iterator< Item > *  iter, size_t  nbIterations = 0, const char *  message = 0, dp::IteratorListener *  listener = 0  )

inline

Create an iterator for the given iterator. If the verbosity is enough, progress bar information can be displayed.

Parameters

[in]	iter	: object to be encapsulated by a potential progress information
[in]	nbIterations	: number of iterations to be done.
[in]	message	: message used if progress information has to be displayed
[in]	listener	: listener to be used; if null, a new one is created

Returns

the created iterator.

dp::IteratorListener * createIteratorListener ( size_t  nbIterations, const char *  message  )

virtual

Creates an iterator listener according to the verbosity level.

Parameters

[in]	nbIterations	: number of iterations to be done
[in]	message	: progression message

Returns

an iterator listener.

virtual void execute ( )

pure virtual

Execution of the algorithm. Abstract method, must be refined in subclasses.

Implemented in SortingCountAlgorithm< span >, MPHFAlgorithm< span, Abundance_t, NodeState_t >, DebloomAlgorithm< span >, BranchingAlgorithm< span, Node, Edge, Graph_t >, BankConverterAlgorithm, and UnitigsConstructionAlgorithm< span >.

virtual dp::IDispatcher* getDispatcher ( )

inlinevirtual

Get an option parser configured with recognized options for the tool

Returns

the options parser instance

virtual IProperties* getInfo ( )

inlinevirtual

Get statistics information about the execution of the tool

Returns

the statistics

virtual IProperties* getInput ( )

inlinevirtual

Get the parsed options as a properties instance

Returns

the parsed options.

std::string getName ( ) const

inline

Get tool name

Returns

the algorithm name.

virtual IProperties* getOutput ( )

inlinevirtual

Get output results as a properties instance

Returns

the output results

virtual IProperties* getSystemInfo ( )

inlinevirtual

Get information about operating system resources used during the execution.

Returns

operating system information.

virtual TimeInfo& getTimeInfo ( )

inlinevirtual

Get a TimeInfo instance for the tool. This object can be used for gathering execution times of some parts of the execute method.

Returns

the time info instance.

std::string getUri ( const std::string &  str )

inlineprotected

Computes the uri from an uri (ie add a prefix if any).

std::string getUriByKey ( const std::string &  key )

inlineprotected

Computes the uri from an uri (ie add a prefix if any).

static int mainloop ( tools::misc::IOptionsParser *  parser, int  argc, char *  argv[]  )

inlinestatic

Utility function for easily running a kmers based algorithms. It ensures that the correct instance of the provided functor is launched, according to the kmer size (known at runtime).

void run

(

)

Run the algorithm, ie. call 'execute'.

void setInput ( IProperties *  input )

inlineprotected

Setters.

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

• /builds/workspace/publish-doc-api-gitlab/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp
• /builds/workspace/publish-doc-api-gitlab/gatb-core/src/gatb/tools/misc/impl/Algorithm.cpp