Parameters controlling execution of the combinatorial algorithm for exploration of a fragment space by layer (CEBL). More...

Inheritance diagram for denoptim.programs.combinatorial.CEBLParameters:

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Collaboration diagram for denoptim.programs.combinatorial.CEBLParameters:

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Public Member Functions
	CEBLParameters ()
	Constructor. More...

ArrayList< DGraph >	getRootGraphs ()

String	getUIDFileName ()

boolean	submitFitnessTask ()

String	getDBRoot ()

void	setDBRoot (String pathname)

int	getNumberOfCPU ()

long	getMaxWait ()

long	getWaitStep ()

int	getMaxLevel ()

boolean	useGivenRoots ()

int	getCheckPointStep ()

String	getCheckPointName ()

CheckPoint	getCheckPoint ()

boolean	restartFromCheckPoint ()

boolean	prepareFilesForTests ()

void	interpretKeyword (String key, String value) throws DENOPTIMException
	Processes a keyword/value pair and assign the related parameters. More...

void	checkParameters () throws DENOPTIMException
	Evaluate consistency of input parameters. More...

void	processParameters () throws DENOPTIMException
	Processes all parameters and initialize related objects. More...

String	getPrintedList ()
	Returns the list of parameters in a string with newline characters as delimiters. More...

Public Member Functions inherited from denoptim.programs.RunTimeParameters
	RunTimeParameters (ParametersType paramType)
	Constructor. More...

String	paramTypeName ()
	Returns a string defining the type the parameters collected here. More...

String	getWorkDirectory ()
	Gets the pathname to the working directory. More...

void	setWorkDirectory (String pathname)
	Gets the pathname to the working directory. More...

String	getLogFilePathname ()
	Gets the pathname to the log file. More...

void	setLogFilePathname (String pathname)
	Sets the pathname to the log file. More...

Logger	getLogger ()
	Get the name of the program specific logger. More...

Logger	startProgramSpecificLogger (String loggerIdentifier) throws SecurityException, IOException
	Starts a logger with the given name. More...

Logger	startProgramSpecificLogger (String loggerIdentifier, boolean toLogFile) throws SecurityException, IOException
	Starts a logger with the given name. More...

Logger	startConsoleLogger (String loggerIdentifier)
	Starts a program-specific logger that prints to System.err stream. More...

int	getVerbosity ()
	Returns the level of verbosity, i.e., the amount of log that we want to print. More...

void	setVerbosity (int l)
	Set the level of verbosity. More...

Randomizer	getRandomizer ()
	Returns the current program-specific randomizer. More...

long	getRandomSeed ()
	Returns the seed. More...

void	setRandomizer (Randomizer rng)
	Sets the randomizer. More...

Randomizer	startRandomizer ()
	Starts a program specific randomizer, i.e., a tool for generating random numbers and taking random decisions. More...

Randomizer	startRandomizer (long seed)
	Starts a program specific randomizer, i.e., a tool for generating random numbers and taking random decisions. More...

void	readParameterFile (String infile) throws DENOPTIMException
	Read the parameter TXT file line by line and interpret its content. More...

void	readParameterLine (String line) throws DENOPTIMException

boolean	containsParameters (ParametersType type)

RunTimeParameters	getParameters (ParametersType type)

void	setParameters (RunTimeParameters otherParams)

void	interpretKeyword (String line) throws DENOPTIMException
	Processes a string looking for keyword and a possibly associated value. More...

abstract void	interpretKeyword (String key, String value) throws DENOPTIMException
	Processes a keyword/value pair and assign the related parameters. More...

abstract void	checkParameters () throws DENOPTIMException
	Evaluate consistency of input parameters. More...

abstract void	processParameters () throws DENOPTIMException
	Processes all parameters and initialize related objects. More...

abstract String	getPrintedList ()
	Returns the list of parameters in a string with newline characters as delimiters. More...

void	printParameters ()
	Print all parameters. More...

Private Member Functions
void	createWorkingDirectory ()

Private Attributes
String	rootGraphsFile = null
	File with user defined list of root graphs. More...

boolean	useGivenRoots = false
	Flag declaring that generation of graphs will use a given list of graphs as starting points for the exploration. More...

ArrayList< DGraph >	rootGraphs
	User defined list of root graphs. More...

String	uidFile = "UID.txt"
	Unique identifier file. More...

boolean	runFitnessTask = false
	Flag: optionally perform an evaluation of the fitness/descriptors on each accepted graph. More...

String	dbRootDir = "."
	Folder containing `DENOPTIMGraph`s sorted by level and reported as `String`s. More...

int	numCPU = 1
	Number of processors. More...

long	maxWait = 600000L
	Maximum wait for completion of a level (millisec) More...

long	waitStep = 5000L
	Time step between each check for completion of a level (millisec) More...

int	maxLevel = 2
	Maximum level accepted: number of frag-frag bond from the origin (i.e., the scaffolds) More...

int	chkptStep = 100
	Number of combinations between every check out of the current position into a checkpoint file. More...

CheckPoint	chkpt = null
	Checkpoint for restarting an interrupted FSE run. More...

String	chkptFile = null
	Name of checkpoint file for restarting an interrupted FSE run. More...

boolean	chkptRestart = false
	Flag defining a restart from checkpoint file. More...

boolean	prepareChkAndSerForTests = false
	Flag requiring generation of the checkpoint files for the testing suite. More...

Additional Inherited Members
Static Public Member Functions inherited from denoptim.programs.RunTimeParameters
static boolean	readYesNoTrueFalse (String s)
	Reads a string searching for any common way to say either yes/true (including shorthand t/y) or no/false (including shorthand f/n either). More...

Public Attributes inherited from denoptim.programs.RunTimeParameters
final String	NL = System.getProperty("line.separator")
	New line character. More...

Protected Member Functions inherited from denoptim.programs.RunTimeParameters
void	checkOtherParameters () throws DENOPTIMException
	Checks any of the parameter collections contained in this instance. More...

void	processOtherParameters () throws DENOPTIMException
	Processes any of the parameter collections contained in this instance. More...

void	ensureFileExistsIfSet (String pathname)
	Ensures a pathname is not empty nor null and that it does lead to an existing file or triggers an error. More...

void	ensureFileExists (String pathname)
	Ensures a pathname does lead to an existing file or triggers an error. More...

void	ensureNotNull (String paramName, String param, String paramKey)
	Ensures that a parameter is not null or triggers an error. More...

void	ensureIsPositive (String paramName, int value, String paramKey)
	Ensures that a parameter is a positive number (x>=0) or triggers an error. More...

void	ensureIsPositiveOrZero (String paramName, int value, String paramKey)
	Ensures that a parameter is a positive number (x>=0) or triggers an error. More...

void	ensureInRange (String paramName, int value, int min, int max, String paramKey)
	Ensures that a parameter is within a range or triggers an error. More...

Protected Attributes inherited from denoptim.programs.RunTimeParameters
boolean	isMaster = true
	Flag signaling this is the master collection of parameters. More...

String	workDir = System.getProperty("user.dir")
	Working directory. More...

String	logFile = "unset"
	Log file. More...

int	verbosity = 0
	Verbosity level for logger. More...

Map< ParametersType, RunTimeParameters >	otherParameters
	Collection of other parameters by type. More...

Detailed Description

Parameters controlling execution of the combinatorial algorithm for exploration of a fragment space by layer (CEBL).

Author: Marco Foscato

Definition at line 48 of file CEBLParameters.java.

Constructor & Destructor Documentation

◆ CEBLParameters()

denoptim.programs.combinatorial.CEBLParameters.CEBLParameters ( )

Constructor.

Definition at line 138 of file CEBLParameters.java.

References denoptim.programs.RunTimeParameters.ParametersType.CEBL_PARAMS.

Member Function Documentation

◆ checkParameters()

void denoptim.programs.combinatorial.CEBLParameters.checkParameters ( ) throws DENOPTIMException

Evaluate consistency of input parameters.

Exceptions

DENOPTIMException

Reimplemented from denoptim.programs.RunTimeParameters.

Definition at line 363 of file CEBLParameters.java.

Referenced by denoptim.programs.combinatorial.FragSpaceExplorer.runProgram().

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◆ createWorkingDirectory()

void denoptim.programs.combinatorial.CEBLParameters.createWorkingDirectory ( )

private

Definition at line 478 of file CEBLParameters.java.

References denoptim.files.FileUtils.addToRecentFiles(), denoptim.files.FileUtils.createDirectory(), denoptim.programs.combinatorial.CEBLParameters.dbRootDir, denoptim.files.FileFormat.FSE_RUN, denoptim.programs.RunTimeParameters.logFile, and denoptim.programs.RunTimeParameters.workDir.

Referenced by denoptim.programs.combinatorial.CEBLParameters.processParameters().

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◆ getCheckPoint()

CheckPoint denoptim.programs.combinatorial.CEBLParameters.getCheckPoint ( )

Definition at line 229 of file CEBLParameters.java.

References denoptim.programs.combinatorial.CEBLParameters.chkpt.

Referenced by denoptim.combinatorial.CombinatorialExplorerByLayer.exploreCombinationsAtGivenLevel(), denoptim.combinatorial.CombinatorialExplorerByLayer.makeCheckPoint(), and denoptim.combinatorial.CombinatorialExplorerByLayer.run().

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◆ getCheckPointName()

String denoptim.programs.combinatorial.CEBLParameters.getCheckPointName ( )

Definition at line 222 of file CEBLParameters.java.

References denoptim.programs.combinatorial.CEBLParameters.chkptFile.

◆ getCheckPointStep()

int denoptim.programs.combinatorial.CEBLParameters.getCheckPointStep ( )

Definition at line 215 of file CEBLParameters.java.

References denoptim.programs.combinatorial.CEBLParameters.chkptStep.

Referenced by denoptim.combinatorial.CombinatorialExplorerByLayer.exploreCombinationsAtGivenLevel().

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◆ getDBRoot()

String denoptim.programs.combinatorial.CEBLParameters.getDBRoot ( )

Definition at line 166 of file CEBLParameters.java.

References denoptim.programs.combinatorial.CEBLParameters.dbRootDir.

Referenced by denoptim.combinatorial.CEBLUtils.getNameOfStorageDir(), denoptim.combinatorial.CEBLUtils.getNameOfStorageFile(), and denoptim.combinatorial.CEBLUtils.getNameOfStorageIndexFile().

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◆ getMaxLevel()

int denoptim.programs.combinatorial.CEBLParameters.getMaxLevel ( )

Definition at line 201 of file CEBLParameters.java.

References denoptim.programs.combinatorial.CEBLParameters.maxLevel.

Referenced by denoptim.combinatorial.CombinatorialExplorerByLayer.run().

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◆ getMaxWait()

long denoptim.programs.combinatorial.CEBLParameters.getMaxWait ( )

Definition at line 187 of file CEBLParameters.java.

References denoptim.programs.combinatorial.CEBLParameters.maxWait.

Referenced by denoptim.combinatorial.CombinatorialExplorerByLayer.run().

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◆ getNumberOfCPU()

int denoptim.programs.combinatorial.CEBLParameters.getNumberOfCPU ( )

Definition at line 180 of file CEBLParameters.java.

References denoptim.programs.combinatorial.CEBLParameters.numCPU.

Referenced by denoptim.combinatorial.CombinatorialExplorerByLayer.CombinatorialExplorerByLayer().

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◆ getPrintedList()

String denoptim.programs.combinatorial.CEBLParameters.getPrintedList ( )

Returns the list of parameters in a string with newline characters as delimiters.

Returns: the list of parameters in a string with newline characters as delimiters.

Reimplemented from denoptim.programs.RunTimeParameters.

Definition at line 506 of file CEBLParameters.java.

References denoptim.programs.RunTimeParameters.NL, denoptim.programs.RunTimeParameters.otherParameters, and denoptim.programs.RunTimeParameters.paramTypeName().

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◆ getRootGraphs()

ArrayList< DGraph > denoptim.programs.combinatorial.CEBLParameters.getRootGraphs ( )

Definition at line 145 of file CEBLParameters.java.

References denoptim.programs.combinatorial.CEBLParameters.rootGraphs.

Referenced by denoptim.combinatorial.CombinatorialExplorerByLayer.exploreCombinationsAtGivenLevel().

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◆ getUIDFileName()

String denoptim.programs.combinatorial.CEBLParameters.getUIDFileName ( )

Definition at line 152 of file CEBLParameters.java.

References denoptim.programs.combinatorial.CEBLParameters.uidFile.

Referenced by denoptim.combinatorial.GraphBuildingTask.sendToFitnessProvider().

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◆ getWaitStep()

long denoptim.programs.combinatorial.CEBLParameters.getWaitStep ( )

Definition at line 194 of file CEBLParameters.java.

References denoptim.programs.combinatorial.CEBLParameters.waitStep.

Referenced by denoptim.combinatorial.CombinatorialExplorerByLayer.run().

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◆ interpretKeyword()

void denoptim.programs.combinatorial.CEBLParameters.interpretKeyword	(	String	key,
		String	value
	)		throws DENOPTIMException

Processes a keyword/value pair and assign the related parameters.

Parameters

key	the keyword as string
value	the value as a string

Exceptions

DENOPTIMException

Reimplemented from denoptim.programs.RunTimeParameters.

Definition at line 256 of file CEBLParameters.java.

◆ prepareFilesForTests()

boolean denoptim.programs.combinatorial.CEBLParameters.prepareFilesForTests ( )

Definition at line 243 of file CEBLParameters.java.

References denoptim.programs.combinatorial.CEBLParameters.prepareChkAndSerForTests.

Referenced by denoptim.combinatorial.CombinatorialExplorerByLayer.exploreCombinationsAtGivenLevel().

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◆ processParameters()

void denoptim.programs.combinatorial.CEBLParameters.processParameters ( ) throws DENOPTIMException

Processes all parameters and initialize related objects.

Exceptions

DENOPTIMException

Reimplemented from denoptim.programs.RunTimeParameters.

Definition at line 436 of file CEBLParameters.java.

References denoptim.logging.StaticLogger.appLogger, denoptim.programs.combinatorial.CEBLParameters.chkpt, denoptim.programs.combinatorial.CEBLParameters.chkptFile, denoptim.programs.combinatorial.CEBLParameters.chkptRestart, denoptim.programs.combinatorial.CEBLParameters.createWorkingDirectory(), denoptim.combinatorial.CEBLUtils.deserializeCheckpoint(), denoptim.constants.DENOPTIMConstants.EOL, denoptim.programs.RunTimeParameters.isMaster, denoptim.programs.RunTimeParameters.logFile, denoptim.programs.RunTimeParameters.processOtherParameters(), denoptim.io.DenoptimIO.readDENOPTIMGraphsFromFile(), denoptim.programs.combinatorial.CEBLParameters.rootGraphs, denoptim.programs.combinatorial.CEBLParameters.rootGraphsFile, denoptim.programs.combinatorial.CEBLParameters.useGivenRoots, and denoptim.programs.RunTimeParameters.workDir.

Referenced by denoptim.programs.combinatorial.FragSpaceExplorer.runProgram().

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◆ restartFromCheckPoint()

boolean denoptim.programs.combinatorial.CEBLParameters.restartFromCheckPoint ( )

Definition at line 236 of file CEBLParameters.java.

References denoptim.programs.combinatorial.CEBLParameters.chkptRestart.

Referenced by denoptim.combinatorial.CombinatorialExplorerByLayer.CombinatorialExplorerByLayer().

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◆ setDBRoot()

void denoptim.programs.combinatorial.CEBLParameters.setDBRoot ( String pathname )

Definition at line 173 of file CEBLParameters.java.

◆ submitFitnessTask()

boolean denoptim.programs.combinatorial.CEBLParameters.submitFitnessTask ( )

Definition at line 159 of file CEBLParameters.java.

References denoptim.programs.combinatorial.CEBLParameters.runFitnessTask.

Referenced by denoptim.combinatorial.GraphBuildingTask.call().

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◆ useGivenRoots()

boolean denoptim.programs.combinatorial.CEBLParameters.useGivenRoots ( )

Definition at line 208 of file CEBLParameters.java.

References denoptim.programs.combinatorial.CEBLParameters.useGivenRoots.

Member Data Documentation

◆ chkpt

CheckPoint denoptim.programs.combinatorial.CEBLParameters.chkpt = null

private

Checkpoint for restarting an interrupted FSE run.

Definition at line 113 of file CEBLParameters.java.

Referenced by denoptim.programs.combinatorial.CEBLParameters.getCheckPoint(), and denoptim.programs.combinatorial.CEBLParameters.processParameters().

◆ chkptFile

String denoptim.programs.combinatorial.CEBLParameters.chkptFile = null

private

Name of checkpoint file for restarting an interrupted FSE run.

Definition at line 118 of file CEBLParameters.java.

Referenced by denoptim.programs.combinatorial.CEBLParameters.checkParameters(), denoptim.programs.combinatorial.CEBLParameters.getCheckPointName(), denoptim.programs.combinatorial.CEBLParameters.interpretKeyword(), and denoptim.programs.combinatorial.CEBLParameters.processParameters().

◆ chkptRestart

boolean denoptim.programs.combinatorial.CEBLParameters.chkptRestart = false

private

Flag defining a restart from checkpoint file.

Definition at line 123 of file CEBLParameters.java.

Referenced by denoptim.programs.combinatorial.CEBLParameters.interpretKeyword(), denoptim.programs.combinatorial.CEBLParameters.processParameters(), and denoptim.programs.combinatorial.CEBLParameters.restartFromCheckPoint().

◆ chkptStep

int denoptim.programs.combinatorial.CEBLParameters.chkptStep = 100

private

Number of combinations between every check out of the current position into a checkpoint file.

Definition at line 108 of file CEBLParameters.java.

Referenced by denoptim.programs.combinatorial.CEBLParameters.checkParameters(), denoptim.programs.combinatorial.CEBLParameters.getCheckPointStep(), and denoptim.programs.combinatorial.CEBLParameters.interpretKeyword().

◆ dbRootDir

String denoptim.programs.combinatorial.CEBLParameters.dbRootDir = "."

private

Folder containing DENOPTIMGraphs sorted by level and reported as Strings.

Definition at line 81 of file CEBLParameters.java.

Referenced by denoptim.programs.combinatorial.CEBLParameters.checkParameters(), denoptim.programs.combinatorial.CEBLParameters.createWorkingDirectory(), denoptim.programs.combinatorial.CEBLParameters.getDBRoot(), and denoptim.programs.combinatorial.CEBLParameters.interpretKeyword().

◆ maxLevel

int denoptim.programs.combinatorial.CEBLParameters.maxLevel = 2

private

Maximum level accepted: number of frag-frag bond from the origin (i.e., the scaffolds)

Definition at line 102 of file CEBLParameters.java.

Referenced by denoptim.programs.combinatorial.CEBLParameters.checkParameters(), denoptim.programs.combinatorial.CEBLParameters.getMaxLevel(), and denoptim.programs.combinatorial.CEBLParameters.interpretKeyword().

◆ maxWait

long denoptim.programs.combinatorial.CEBLParameters.maxWait = 600000L

private

Maximum wait for completion of a level (millisec)

Definition at line 91 of file CEBLParameters.java.

Referenced by denoptim.programs.combinatorial.CEBLParameters.getMaxWait(), and denoptim.programs.combinatorial.CEBLParameters.interpretKeyword().

◆ numCPU

int denoptim.programs.combinatorial.CEBLParameters.numCPU = 1

private

Number of processors.

Definition at line 86 of file CEBLParameters.java.

Referenced by denoptim.programs.combinatorial.CEBLParameters.checkParameters(), denoptim.programs.combinatorial.CEBLParameters.getNumberOfCPU(), and denoptim.programs.combinatorial.CEBLParameters.interpretKeyword().

◆ prepareChkAndSerForTests

boolean denoptim.programs.combinatorial.CEBLParameters.prepareChkAndSerForTests = false

private

Flag requiring generation of the checkpoint files for the testing suite.

When true allows to stop the asyncronous, parallelized exploration of a fragment space so that checkpoint files and serialized graphs can be generated and used to prepare the test suite.

Definition at line 131 of file CEBLParameters.java.

Referenced by denoptim.programs.combinatorial.CEBLParameters.interpretKeyword(), and denoptim.programs.combinatorial.CEBLParameters.prepareFilesForTests().

◆ rootGraphs

ArrayList<DGraph> denoptim.programs.combinatorial.CEBLParameters.rootGraphs

private

User defined list of root graphs.

Definition at line 64 of file CEBLParameters.java.

Referenced by denoptim.programs.combinatorial.CEBLParameters.getRootGraphs(), and denoptim.programs.combinatorial.CEBLParameters.processParameters().

◆ rootGraphsFile

String denoptim.programs.combinatorial.CEBLParameters.rootGraphsFile = null

private

File with user defined list of root graphs.

Definition at line 53 of file CEBLParameters.java.

Referenced by denoptim.programs.combinatorial.CEBLParameters.checkParameters(), denoptim.programs.combinatorial.CEBLParameters.interpretKeyword(), and denoptim.programs.combinatorial.CEBLParameters.processParameters().

◆ runFitnessTask

boolean denoptim.programs.combinatorial.CEBLParameters.runFitnessTask = false

private

Flag: optionally perform an evaluation of the fitness/descriptors on each accepted graph.

Definition at line 75 of file CEBLParameters.java.

Referenced by denoptim.programs.combinatorial.CEBLParameters.checkParameters(), and denoptim.programs.combinatorial.CEBLParameters.submitFitnessTask().

◆ uidFile

String denoptim.programs.combinatorial.CEBLParameters.uidFile = "UID.txt"

private

Unique identifier file.

Definition at line 69 of file CEBLParameters.java.

Referenced by denoptim.programs.combinatorial.CEBLParameters.getUIDFileName(), and denoptim.programs.combinatorial.CEBLParameters.interpretKeyword().

◆ useGivenRoots

boolean denoptim.programs.combinatorial.CEBLParameters.useGivenRoots = false

private

Flag declaring that generation of graphs will use a given list of graphs as starting points for the exploration.

Definition at line 59 of file CEBLParameters.java.

Referenced by denoptim.combinatorial.CombinatorialExplorerByLayer.exploreCombinationsAtGivenLevel(), denoptim.programs.combinatorial.CEBLParameters.interpretKeyword(), denoptim.programs.combinatorial.CEBLParameters.processParameters(), and denoptim.programs.combinatorial.CEBLParameters.useGivenRoots().

◆ waitStep

long denoptim.programs.combinatorial.CEBLParameters.waitStep = 5000L

private

Time step between each check for completion of a level (millisec)

Definition at line 96 of file CEBLParameters.java.

Referenced by denoptim.programs.combinatorial.CEBLParameters.getWaitStep(), and denoptim.programs.combinatorial.CEBLParameters.interpretKeyword().

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

/github/workspace/src/main/java/denoptim/programs/combinatorial/CEBLParameters.java

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CEBLParameters()

Member Function Documentation

◆ checkParameters()

◆ createWorkingDirectory()

◆ getCheckPoint()

◆ getCheckPointName()

◆ getCheckPointStep()

◆ getDBRoot()

◆ getMaxLevel()

◆ getMaxWait()

◆ getNumberOfCPU()

◆ getPrintedList()

◆ getRootGraphs()

◆ getUIDFileName()

◆ getWaitStep()

◆ interpretKeyword()

◆ prepareFilesForTests()

◆ processParameters()

◆ restartFromCheckPoint()

◆ setDBRoot()

◆ submitFitnessTask()

◆ useGivenRoots()

Member Data Documentation

◆ chkpt

◆ chkptFile

◆ chkptRestart

◆ chkptStep

◆ dbRootDir

◆ maxLevel

◆ maxWait

◆ numCPU

◆ prepareChkAndSerForTests

◆ rootGraphs

◆ rootGraphsFile

◆ runFitnessTask

◆ uidFile

◆ useGivenRoots

◆ waitStep