Collection of parameters controlling the behavior of the software. More...

Inheritance diagram for denoptim.programs.RunTimeParameters:

Collaboration diagram for denoptim.programs.RunTimeParameters:

Classes
enum	ParametersType
	Identifier of the type of parameters. More...

Public Member Functions
	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...

Static Public Member Functions
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
final String	NL = System.getProperty("line.separator")
	New line character. More...

Protected Member Functions
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
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...

Private Member Functions
void	setLogger (Logger logger)
	Set the name of the program specific logger. More...

Level	verbosityTologLevel ()

Static Private Member Functions
static RunTimeParameters	getInstanceFor (ParametersType paramType)
	Builds the implementation of this class suitable to allocate parameters of the given type. More...

Private Attributes
Logger	logger = Logger.getLogger("DummyLogger")
	Program-specific logger. More...

Randomizer	rng = null
	Program-specific random numbers and random decisions generator. More...

ParametersType	paramType = null
	The type of parameters collected in this instance. More...

Detailed Description

Collection of parameters controlling the behavior of the software.

These parameters have a default value and are optionally defined at startup by reading in input parameter file. Parameters are collected in a hierarchical structure so that those parameters that determine the primary behavior of the software, i.e., define the RunType, determine also the type of the main parameter collector, i.e., any one of the implementations of this class. Other parameters, such as those defining the settings of functions used by the main program, are collected as secondary parameters that can be accessed via the primary one by means of the getParameters(ParametersType) method.

Author: Marco Foscato

Definition at line 67 of file RunTimeParameters.java.

Constructor & Destructor Documentation

◆ RunTimeParameters()

denoptim.programs.RunTimeParameters.RunTimeParameters ( ParametersType paramType )

Constructor.

Parameters

paramType the type of parameters this instance is meant to collect.

Definition at line 270 of file RunTimeParameters.java.

References denoptim.programs.RunTimeParameters.paramType.

Referenced by denoptim.programs.RunTimeParameters.getInstanceFor().

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Member Function Documentation

◆ checkOtherParameters()

void denoptim.programs.RunTimeParameters.checkOtherParameters ( ) throws DENOPTIMException

protected

Checks any of the parameter collections contained in this instance.

Exceptions

DENOPTIMException

Definition at line 889 of file RunTimeParameters.java.

References denoptim.programs.RunTimeParameters.otherParameters.

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◆ checkParameters()

abstract void denoptim.programs.RunTimeParameters.checkParameters ( ) throws DENOPTIMException

abstract

Evaluate consistency of input parameters.

Exceptions

DENOPTIMException

◆ containsParameters()

boolean denoptim.programs.RunTimeParameters.containsParameters ( ParametersType type )

Parameters

type	the type of parameter to search for.

Returns: true if the parameter is found among those collections of embedded parameters that are contained in this instance.

Definition at line 779 of file RunTimeParameters.java.

References denoptim.programs.RunTimeParameters.otherParameters.

Referenced by denoptim.molecularmodeling.MultiMolecularModelBuilder.buildMulti3DStructure(), denoptim.molecularmodeling.RingClosureTool.closeRings(), denoptim.combinatorial.CombinatorialExplorerByLayer.CombinatorialExplorerByLayer(), denoptim.programs.fitnessevaluator.FitnessEvaluationTask.FitnessEvaluationTask(), denoptim.ga.EvolutionaryAlgorithm.initializePopulation(), denoptim.ga.OffspringEvaluationTask.OffspringEvaluationTask(), denoptim.ga.EAUtils.performFBCC(), denoptim.programs.denovo.GAParameters.processParameters(), denoptim.programs.genetweeker.GeneOpsRunnerParameters.processParameters(), denoptim.programs.genetweeker.GeneOpsRunner.runMutation(), denoptim.programs.genetweeker.GeneOpsRunner.runProgram(), and denoptim.programs.grapheditor.GraphEditor.runProgram().

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◆ ensureFileExists()

void denoptim.programs.RunTimeParameters.ensureFileExists ( String pathname )

protected

Ensures a pathname does lead to an existing file or triggers an error.

This is meant for checking initialization settings and does not print in the program specific log file.

Definition at line 1001 of file RunTimeParameters.java.

References denoptim.files.FileUtils.checkExists().

Referenced by denoptim.programs.fragmenter.FragmenterParameters.checkParameters(), and denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.checkParameters().

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◆ ensureFileExistsIfSet()

void denoptim.programs.RunTimeParameters.ensureFileExistsIfSet ( String pathname )

protected

Ensures a pathname is not empty nor null and that it does lead to an existing file or triggers an error.

This is meant for checking initialization settings and does not print in the program specific log file.

Definition at line 982 of file RunTimeParameters.java.

References denoptim.files.FileUtils.checkExists().

Referenced by denoptim.programs.fragmenter.FragmenterParameters.checkParameters().

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◆ ensureInRange()

void denoptim.programs.RunTimeParameters.ensureInRange	(	String	paramName,
		int	value,
		int	min,
		int	max,
		String	paramKey
	)

protected

Ensures that a parameter is within a range or triggers an error.

This is meant for checking initialization settings and does not print in the program specific log file.

Definition at line 1074 of file RunTimeParameters.java.

◆ ensureIsPositive()

void denoptim.programs.RunTimeParameters.ensureIsPositive	(	String	paramName,
		int	value,
		String	paramKey
	)

protected

Ensures that a parameter is a positive number (x>=0) or triggers an error.

This is meant for checking initialization settings and does not print in the program specific log file.

Definition at line 1035 of file RunTimeParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.checkParameters().

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◆ ensureIsPositiveOrZero()

void denoptim.programs.RunTimeParameters.ensureIsPositiveOrZero	(	String	paramName,
		int	value,
		String	paramKey
	)

protected

Ensures that a parameter is a positive number (x>=0) or triggers an error.

This is meant for checking initialization settings and does not print in the program specific log file.

Definition at line 1054 of file RunTimeParameters.java.

◆ ensureNotNull()

void denoptim.programs.RunTimeParameters.ensureNotNull	(	String	paramName,
		String	param,
		String	paramKey
	)

protected

Ensures that a parameter is not null or triggers an error.

This is meant for checking initialization settings and does not print in the program specific log file.

Definition at line 1017 of file RunTimeParameters.java.

Referenced by denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.checkParameters().

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◆ getInstanceFor()

static RunTimeParameters denoptim.programs.RunTimeParameters.getInstanceFor ( ParametersType paramType )

staticprivate

Builds the implementation of this class suitable to allocate parameters of the given type.

Parameters

paramType the type of parameters to allocate in the instance to create.

Returns: the instance of the proper type.

Definition at line 758 of file RunTimeParameters.java.

References denoptim.programs.RunTimeParameters.ParametersType.getImplementation(), denoptim.programs.RunTimeParameters.paramType, and denoptim.programs.RunTimeParameters.RunTimeParameters().

Referenced by denoptim.programs.RunTimeParameters.readParameterLine().

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◆ getLogFilePathname()

String denoptim.programs.RunTimeParameters.getLogFilePathname ( )

Gets the pathname to the log file.

Returns

Definition at line 320 of file RunTimeParameters.java.

References denoptim.programs.RunTimeParameters.logFile.

Referenced by denoptim.programs.denovo.GAParametersTest.testLogging().

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◆ getLogger()

Logger denoptim.programs.RunTimeParameters.getLogger ( )

Get the name of the program specific logger.

Definition at line 341 of file RunTimeParameters.java.

References denoptim.programs.RunTimeParameters.logger.

◆ getParameters()

RunTimeParameters denoptim.programs.RunTimeParameters.getParameters ( ParametersType type )

Parameters

type	the type of embedded parameters to search for.

Returns: the requested parameter, or null.

Definition at line 790 of file RunTimeParameters.java.

References denoptim.programs.RunTimeParameters.otherParameters.

Referenced by denoptim.ga.GraphOperations.addRing(), denoptim.ga.GraphOperations.attachFragmentInClosableChain(), denoptim.molecularmodeling.MultiMolecularModelBuilder.build3DTree(), denoptim.ga.EAUtils.buildCandidateByFragmentingMolecule(), denoptim.ga.EAUtils.buildCandidateByMutation(), denoptim.ga.EAUtils.buildCandidateFromScratch(), denoptim.ga.EAUtils.buildCandidatesByXOver(), denoptim.ga.EAUtils.buildGraph(), denoptim.molecularmodeling.MultiMolecularModelBuilder.buildMulti3DStructure(), denoptim.graph.DGraph.checkConsistency(), denoptim.molecularmodeling.RingClosureTool.closeRings(), denoptim.combinatorial.CombinatorialExplorerByLayer.CombinatorialExplorerByLayer(), denoptim.ga.EvolutionaryAlgorithm.evolvePopulation(), denoptim.ga.GraphOperations.extendGraph(), denoptim.programs.fitnessevaluator.FitnessEvaluationTask.FitnessEvaluationTask(), denoptim.combinatorial.GraphBuildingTask.GraphBuildingTask(), denoptim.ga.EvolutionaryAlgorithm.initializePopulation(), denoptim.graph.DGraph.makeAllGraphsWithDifferentRingSets(), denoptim.ga.OffspringEvaluationTask.OffspringEvaluationTask(), denoptim.ga.EAUtils.performFBCC(), denoptim.ga.GraphOperations.performMutation(), denoptim.ga.Population.Population(), denoptim.ga.EvolutionaryAlgorithm.processInitialPopCandidate(), denoptim.programs.denovo.GAParameters.processParameters(), denoptim.ga.EvolutionaryAlgorithm.run(), denoptim.programs.genetweeker.GeneOpsRunner.runMutation(), denoptim.programs.genetweeker.GeneOpsRunner.runProgram(), denoptim.programs.grapheditor.GraphEditor.runProgram(), and denoptim.ga.EAUtils.setupRings().

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◆ getPrintedList()

abstract String denoptim.programs.RunTimeParameters.getPrintedList ( )

abstract

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.

Referenced by denoptim.programs.RunTimeParameters.printParameters().

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◆ getRandomizer()

Randomizer denoptim.programs.RunTimeParameters.getRandomizer ( )

Returns the current program-specific randomizer.

If no such tool has been configured, then it creates one using a new and uncontrollable random seed.

Returns: the current and program-specific tool for random number and random decision generation.

Definition at line 590 of file RunTimeParameters.java.

References denoptim.programs.RunTimeParameters.otherParameters, and denoptim.programs.RunTimeParameters.rng.

Referenced by denoptim.fragspace.FragmentSpace.addFusedRingsToFragmentLibrary(), denoptim.ga.GraphOperations.attachFragmentInClosableChain(), denoptim.molecularmodeling.MultiMolecularModelBuilder.build3DTree(), denoptim.combinatorial.GraphBuildingTask.call(), denoptim.ga.OffspringEvaluationTask.call(), denoptim.programs.fitnessevaluator.FitnessEvaluationTask.call(), denoptim.ga.EAUtils.chooseGenerationMethod(), denoptim.graph.rings.PathClosabilityTools.evaluate3DPathClosability(), denoptim.ga.GraphOperations.extendGraph(), denoptim.fragspace.FragmentSpace.getCappingFragment(), denoptim.fragspace.FragmentSpace.getRandomizer(), denoptim.ga.EvolutionaryAlgorithm.makeOffspringB(), denoptim.fragspace.FragmentSpace.makeRandomScaffold(), denoptim.graph.rings.RandomCombOfRingsIterator.next(), denoptim.ga.EAUtils.performFBCC(), denoptim.ga.SelectionHelper.performRandomSelection(), denoptim.ga.SelectionHelper.performRWS(), denoptim.ga.SelectionHelper.performSUS(), denoptim.ga.SelectionHelper.performTournamentSelection(), denoptim.task.FitnessTask.runFitnessProvider(), denoptim.programs.genetweeker.GeneOpsRunner.runMutation(), denoptim.programs.grapheditor.GraphEditor.runProgram(), denoptim.programs.genetweeker.GeneOpsRunner.runXOver(), and denoptim.fragspace.FragmentSpaceTest.testUseWholeMolGeometryForExtractedTemplates().

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◆ getRandomSeed()

long denoptim.programs.RunTimeParameters.getRandomSeed ( )

Returns the seed.

Returns

Definition at line 618 of file RunTimeParameters.java.

References denoptim.utils.Randomizer.getSeed(), and denoptim.programs.RunTimeParameters.rng.

Referenced by denoptim.programs.denovo.GAParameters.processParameters().

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◆ getVerbosity()

int denoptim.programs.RunTimeParameters.getVerbosity ( )

Returns the level of verbosity, i.e., the amount of log that we want to print.

Returns: the level of verbosity.

Reimplemented in denoptim.graph.rings.RingClosureParameters.

Definition at line 548 of file RunTimeParameters.java.

References denoptim.programs.RunTimeParameters.verbosity.

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

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◆ getWorkDirectory()

String denoptim.programs.RunTimeParameters.getWorkDirectory ( )

Gets the pathname to the working directory.

Returns: the pathname

Definition at line 298 of file RunTimeParameters.java.

References denoptim.programs.RunTimeParameters.workDir.

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◆ interpretKeyword() [1/2]

abstract void denoptim.programs.RunTimeParameters.interpretKeyword	(	String	key,
		String	value
	)		throws DENOPTIMException

abstract

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

Parameters

key	the keyword as string
value	the value as a string

Exceptions

DENOPTIMException is the parameter cannot be configured from the given value.

◆ interpretKeyword() [2/2]

void denoptim.programs.RunTimeParameters.interpretKeyword ( String line ) throws DENOPTIMException

Processes a string looking for keyword and a possibly associated value.

Parameters

line	the string to parse

Exceptions

DENOPTIMException

Definition at line 841 of file RunTimeParameters.java.

References denoptim.programs.RunTimeParameters.interpretKeyword(), denoptim.programs.RunTimeParameters.ParametersType.keywordRoot, and denoptim.programs.RunTimeParameters.paramType.

Referenced by denoptim.programs.RunTimeParameters.interpretKeyword(), and denoptim.programs.RunTimeParameters.readParameterLine().

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◆ paramTypeName()

String denoptim.programs.RunTimeParameters.paramTypeName ( )

Returns a string defining the type the parameters collected here.

Returns: a string defining the type the parameters collected here.

Definition at line 287 of file RunTimeParameters.java.

References denoptim.programs.RunTimeParameters.paramType.

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◆ printParameters()

void denoptim.programs.RunTimeParameters.printParameters ( )

Print all parameters.

Definition at line 965 of file RunTimeParameters.java.

References denoptim.programs.RunTimeParameters.getPrintedList(), denoptim.programs.RunTimeParameters.logger, and denoptim.programs.RunTimeParameters.NL.

Referenced by denoptim.programs.combinatorial.FragSpaceExplorer.runProgram(), denoptim.programs.denovo.GARunner.runProgram(), denoptim.programs.fitnessevaluator.FitnessRunner.runProgram(), denoptim.programs.fragmenter.Fragmenter.runProgram(), denoptim.programs.genetweeker.GeneOpsRunner.runProgram(), denoptim.programs.grapheditor.GraphEditor.runProgram(), denoptim.programs.graphlisthandler.GraphListsHandler.runProgram(), and denoptim.programs.moldecularmodelbuilder.MolecularModelBuilder.runProgram().

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◆ processOtherParameters()

void denoptim.programs.RunTimeParameters.processOtherParameters ( ) throws DENOPTIMException

protected

Processes any of the parameter collections contained in this instance.

Exceptions

DENOPTIMException

Definition at line 911 of file RunTimeParameters.java.

References denoptim.programs.RunTimeParameters.otherParameters.

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◆ processParameters()

abstract void denoptim.programs.RunTimeParameters.processParameters ( ) throws DENOPTIMException

abstract

Processes all parameters and initialize related objects.

Exceptions

DENOPTIMException

◆ readParameterFile()

void denoptim.programs.RunTimeParameters.readParameterFile ( String infile ) throws DENOPTIMException

Read the parameter TXT file line by line and interpret its content.

Parameters

infile

Exceptions

DENOPTIMException

Definition at line 680 of file RunTimeParameters.java.

References denoptim.programs.RunTimeParameters.readParameterLine().

Referenced by denoptim.programs.combinatorial.FragSpaceExplorer.runProgram(), denoptim.programs.denovo.GARunner.runProgram(), denoptim.programs.fitnessevaluator.FitnessRunner.runProgram(), denoptim.programs.fragmenter.Fragmenter.runProgram(), denoptim.programs.genetweeker.GeneOpsRunner.runProgram(), denoptim.programs.grapheditor.GraphEditor.runProgram(), denoptim.programs.graphlisthandler.GraphListsHandler.runProgram(), denoptim.programs.isomorphism.Isomorphism.runProgram(), and denoptim.programs.moldecularmodelbuilder.MolecularModelBuilder.runProgram().

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◆ readParameterLine()

void denoptim.programs.RunTimeParameters.readParameterLine ( String line ) throws DENOPTIMException

Parameters

line	the line to try to interpret.

Exceptions

DENOPTIMException if the parameter could be read but not interpreted, i.e., any wrong format of syntax.

Definition at line 720 of file RunTimeParameters.java.

References denoptim.programs.RunTimeParameters.getInstanceFor(), denoptim.programs.RunTimeParameters.interpretKeyword(), denoptim.programs.RunTimeParameters.ParametersType.keywordRoot, denoptim.programs.RunTimeParameters.otherParameters, and denoptim.programs.RunTimeParameters.paramType.

Referenced by denoptim.gui.FSParamsDialog.makeFragSpace(), denoptim.ga.PopulationTest.prepare(), denoptim.programs.RunTimeParameters.readParameterFile(), and denoptim.programs.denovo.GAParametersTest.testLogging().

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◆ readYesNoTrueFalse()

static boolean denoptim.programs.RunTimeParameters.readYesNoTrueFalse ( String s )

static

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).

This method is case insensitive, and the string is trimmed.

Parameters

s	the string to interpret.

Returns: true for 'true/yes'.

Definition at line 491 of file RunTimeParameters.java.

Referenced by denoptim.gui.FitnessParametersForm.importSingleParameter(), denoptim.fitness.FitnessParameters.interpretKeyword(), denoptim.programs.denovo.GAParameters.interpretKeyword(), and denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword().

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◆ setLogFilePathname()

void denoptim.programs.RunTimeParameters.setLogFilePathname ( String pathname )

Sets the pathname to the log file.

Parameters

pathname the new value of pathname to the log file.

Definition at line 331 of file RunTimeParameters.java.

◆ setLogger()

void denoptim.programs.RunTimeParameters.setLogger ( Logger logger )

private

Set the name of the program specific logger.

This method should only be used by subclasses that need to set the logger for embedded parameters collections.

Parameters

logger the new logger.

Definition at line 354 of file RunTimeParameters.java.

References denoptim.programs.RunTimeParameters.logger, and denoptim.programs.RunTimeParameters.otherParameters.

◆ setParameters()

void denoptim.programs.RunTimeParameters.setParameters ( RunTimeParameters otherParams )

Parameters

otherParams the parameters to add/set as other in this collection.

Definition at line 800 of file RunTimeParameters.java.

References denoptim.programs.RunTimeParameters.otherParameters, and denoptim.programs.RunTimeParameters.paramType.

Referenced by denoptim.ga.PopulationTest.prepare(), denoptim.programs.genetweeker.GeneOpsRunnerParameters.processParameters(), denoptim.programs.genetweeker.GeneOpsRunner.runMutation(), denoptim.ga.GraphOperationsTest.testAddRing(), denoptim.ga.EAUtilsTest.testAvoidRedundantXOver(), denoptim.ga.EAUtilsTest.testBuildGraphFromTemplateScaffold(), denoptim.ga.GraphOperationsTest.testExtendGraph(), and denoptim.io.DenoptimIOTest.testReadGenerationFromSummary().

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◆ setRandomizer()

void denoptim.programs.RunTimeParameters.setRandomizer ( Randomizer rng )

Sets the randomizer.

This method should only be used by subclasses that need to set the randomizer in embedded parameters collections.

Definition at line 630 of file RunTimeParameters.java.

References denoptim.programs.RunTimeParameters.otherParameters, and denoptim.programs.RunTimeParameters.rng.

Referenced by denoptim.ga.SeelctionHelperTest.testPerformSUS().

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◆ setVerbosity()

void denoptim.programs.RunTimeParameters.setVerbosity ( int l )

Set the level of verbosity.

If any associated logger exists, the level is set accordingly. The change affects all embedded sets of parameters. The integer is translated in a Level so that -3 (or lower) corresponds to Level#OFF, 0 is the normal Level#INFO, and 3 (or higher) corresponds to Level#FINEST.

Definition at line 563 of file RunTimeParameters.java.

References denoptim.programs.RunTimeParameters.logger, denoptim.programs.RunTimeParameters.otherParameters, and denoptim.programs.RunTimeParameters.verbosityTologLevel().

Referenced by denoptim.fragmenter.FragmentClustererTest.testCluster().

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◆ setWorkDirectory()

void denoptim.programs.RunTimeParameters.setWorkDirectory ( String pathname )

Gets the pathname to the working directory.

Parameters

pathname the new value of the working directory pathname.

Definition at line 309 of file RunTimeParameters.java.

Referenced by denoptim.programs.combinatorial.FragSpaceExplorer.runProgram(), denoptim.programs.fitnessevaluator.FitnessRunner.runProgram(), denoptim.programs.fragmenter.Fragmenter.runProgram(), denoptim.programs.moldecularmodelbuilder.MolecularModelBuilder.runProgram(), and denoptim.fragmenter.ParallelFragmentationAlgorithmTest.testSplitInputForThreads().

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◆ startConsoleLogger()

Logger denoptim.programs.RunTimeParameters.startConsoleLogger ( String loggerIdentifier )

Starts a program-specific logger that prints to System.err stream.

Parameters

loggerIdentifier

Returns

Definition at line 451 of file RunTimeParameters.java.

References denoptim.programs.RunTimeParameters.logger, denoptim.programs.RunTimeParameters.otherParameters, denoptim.programs.RunTimeParameters.verbosity, and denoptim.programs.RunTimeParameters.verbosityTologLevel().

Referenced by denoptim.gui.GUIVertexInspector.dialogToDefineCuttingRules(), and denoptim.fragmenter.FragmentClustererTest.testCluster().

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◆ startProgramSpecificLogger() [1/2]

Logger denoptim.programs.RunTimeParameters.startProgramSpecificLogger ( String loggerIdentifier ) throws SecurityException, IOException

Starts a logger with the given name.

The name is saved among the parameters and the logger can be obtained from static Logger#getLogger(String) method using the value of loggerIdentifier or by RunTimeParameters#getLogger(). All parameter collectors embedded in this one will inherit the logger. By default the logger that is created does dump its log into the pathname identified by the RunTimeParameters#logFile field of this instance.

Parameters

loggerIdentifier the string identifying the program-specific logger.

Exceptions

IOException
SecurityException

Definition at line 378 of file RunTimeParameters.java.

References denoptim.programs.RunTimeParameters.startProgramSpecificLogger().

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◆ startProgramSpecificLogger() [2/2]

Logger denoptim.programs.RunTimeParameters.startProgramSpecificLogger	(	String	loggerIdentifier,
		boolean	toLogFile
	)		throws SecurityException, IOException

Starts a logger with the given name.

The name is saved among the parameters and the logger can be obtained from static Logger#getLogger(String) method using the value of loggerIdentifier or by RunTimeParameters#getLogger(). All parameter collectors embedded in this one will inherit the logger.

Parameters

loggerIdentifier	the string identifying the program-specific logger.
toLogFile	with `true` we dump the log to a file. The pathname of such file must have been configured in this collection of parameters as the `RunTimeParameters#logFile` field. With `false` we log on standard output.

Exceptions

IOException
SecurityException

Definition at line 400 of file RunTimeParameters.java.

References denoptim.programs.RunTimeParameters.logFile, denoptim.programs.RunTimeParameters.logger, denoptim.programs.RunTimeParameters.otherParameters, denoptim.programs.RunTimeParameters.verbosity, and denoptim.programs.RunTimeParameters.verbosityTologLevel().

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◆ startRandomizer() [1/2]

Randomizer denoptim.programs.RunTimeParameters.startRandomizer ( )

Starts a program specific randomizer, i.e., a tool for generating random numbers and taking random decisions.

Parameters

seed	the random seed.

Definition at line 646 of file RunTimeParameters.java.

References denoptim.programs.RunTimeParameters.otherParameters, and denoptim.programs.RunTimeParameters.rng.

Referenced by denoptim.programs.denovo.GAParameters.processParameters().

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◆ startRandomizer() [2/2]

Randomizer denoptim.programs.RunTimeParameters.startRandomizer ( long seed )

Starts a program specific randomizer, i.e., a tool for generating random numbers and taking random decisions.

Parameters

seed	the random seed.

Definition at line 663 of file RunTimeParameters.java.

References denoptim.programs.RunTimeParameters.otherParameters, and denoptim.programs.RunTimeParameters.rng.

◆ verbosityTologLevel()

Level denoptim.programs.RunTimeParameters.verbosityTologLevel ( )

private

Definition at line 513 of file RunTimeParameters.java.

References denoptim.programs.RunTimeParameters.verbosity.

Referenced by denoptim.programs.RunTimeParameters.setVerbosity(), denoptim.programs.RunTimeParameters.startConsoleLogger(), and denoptim.programs.RunTimeParameters.startProgramSpecificLogger().

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Member Data Documentation

◆ isMaster

boolean denoptim.programs.RunTimeParameters.isMaster = true

protected

Flag signaling this is the master collection of parameters.

The master collection is the one with the type that corresponds to the type of program task. A parameters collection is master if it may contain other collections without being itself contained in any other collection.

Definition at line 76 of file RunTimeParameters.java.

Referenced by denoptim.programs.combinatorial.CEBLParameters.processParameters(), denoptim.programs.denovo.GAParameters.processParameters(), and denoptim.programs.fragmenter.FragmenterParameters.processParameters().

◆ logFile

String denoptim.programs.RunTimeParameters.logFile = "unset"

protected

Log file.

Definition at line 86 of file RunTimeParameters.java.

◆ logger

Logger denoptim.programs.RunTimeParameters.logger = Logger.getLogger("DummyLogger")

private

Program-specific logger.

Note that initialization errors in input parameters are detected prior to starting the logger. Also, the logger is initialized to avoid null during unit tests. In any proper run, this logger should be overwritten by a call to startProgramSpecificLogger(String).

Definition at line 95 of file RunTimeParameters.java.

Referenced by denoptim.programs.RunTimeParameters.getLogger(), denoptim.programs.RunTimeParameters.printParameters(), denoptim.programs.RunTimeParameters.setLogger(), denoptim.programs.RunTimeParameters.setVerbosity(), denoptim.programs.RunTimeParameters.startConsoleLogger(), and denoptim.programs.RunTimeParameters.startProgramSpecificLogger().

◆ NL

final String denoptim.programs.RunTimeParameters.NL = System.getProperty("line.separator")

New line character.

Definition at line 262 of file RunTimeParameters.java.

◆ otherParameters

Map<ParametersType, RunTimeParameters> denoptim.programs.RunTimeParameters.otherParameters

protected

Initial value:

=

new HashMap<ParametersType, RunTimeParameters>()

Collection of other parameters by type.

Definition at line 112 of file RunTimeParameters.java.

◆ paramType

ParametersType denoptim.programs.RunTimeParameters.paramType = null

private

The type of parameters collected in this instance.

Definition at line 118 of file RunTimeParameters.java.

Referenced by denoptim.fragspace.FragmentSpaceParameters.FragmentSpaceParameters(), denoptim.programs.RunTimeParameters.getInstanceFor(), denoptim.programs.RunTimeParameters.interpretKeyword(), denoptim.programs.RunTimeParameters.paramTypeName(), denoptim.programs.RunTimeParameters.readParameterLine(), denoptim.programs.RunTimeParameters.RunTimeParameters(), and denoptim.programs.RunTimeParameters.setParameters().

◆ rng

Randomizer denoptim.programs.RunTimeParameters.rng = null

private

Program-specific random numbers and random decisions generator.

Definition at line 100 of file RunTimeParameters.java.

Referenced by denoptim.programs.RunTimeParameters.getRandomizer(), denoptim.programs.RunTimeParameters.getRandomSeed(), denoptim.programs.RunTimeParameters.setRandomizer(), and denoptim.programs.RunTimeParameters.startRandomizer().

◆ verbosity

int denoptim.programs.RunTimeParameters.verbosity = 0

protected

Verbosity level for logger.

This is used to help the user setting the Level of the Logger without knowing the names of the logging levels.

Definition at line 107 of file RunTimeParameters.java.

◆ workDir

String denoptim.programs.RunTimeParameters.workDir = System.getProperty("user.dir")

protected

Working directory.

Definition at line 81 of file RunTimeParameters.java.

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

/github/workspace/src/main/java/denoptim/programs/RunTimeParameters.java

Classes

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Private Member Functions

Static Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ RunTimeParameters()

Member Function Documentation

◆ checkOtherParameters()

◆ checkParameters()

◆ containsParameters()

◆ ensureFileExists()

◆ ensureFileExistsIfSet()

◆ ensureInRange()

◆ ensureIsPositive()

◆ ensureIsPositiveOrZero()

◆ ensureNotNull()

◆ getInstanceFor()

◆ getLogFilePathname()

◆ getLogger()

◆ getParameters()

◆ getPrintedList()

◆ getRandomizer()

◆ getRandomSeed()

◆ getVerbosity()

◆ getWorkDirectory()

◆ interpretKeyword() [1/2]

◆ interpretKeyword() [2/2]

◆ paramTypeName()

◆ printParameters()

◆ processOtherParameters()

◆ processParameters()

◆ readParameterFile()

◆ readParameterLine()

◆ readYesNoTrueFalse()

◆ setLogFilePathname()

◆ setLogger()

◆ setParameters()

◆ setRandomizer()

◆ setVerbosity()

◆ setWorkDirectory()

◆ startConsoleLogger()

◆ startProgramSpecificLogger() [1/2]

◆ startProgramSpecificLogger() [2/2]

◆ startRandomizer() [1/2]

◆ startRandomizer() [2/2]

◆ verbosityTologLevel()

Member Data Documentation

◆ isMaster

◆ logFile

◆ logger

◆ NL

◆ otherParameters

◆ paramType

◆ rng

◆ verbosity

◆ workDir