Task that assesses the fitness of a given graph. More...

Inheritance diagram for denoptim.task.FitnessTask:

Collaboration diagram for denoptim.task.FitnessTask:

Public Member Functions
	FitnessTask (FitnessParameters settings, Candidate c)

Public Member Functions inherited from denoptim.task.Task
	Task (final int id)

int	getId ()

void	setVerbosity (int verbosity)
	Set the verbosity: i.e., amount of log printed by this class. More...

void	setWorkSpace (File workDir)
	Sets the pathname of the work space, i.e., the location where the task is supposed to use move to or to threat as the result of "pwd" at runtime. More...

boolean	isCompleted ()

boolean	foundException ()

Throwable	getException ()

String	getErrorMessage ()

void	stopTask ()
	Stop the task if not already completed. More...

String	toString ()
	Returns a string identifying this task by its ID and reporting whether an exception has been thrown and if the tasks is completed. More...

void	setNotify (boolean notify)

Protected Member Functions
void	runFitnessProvider () throws DENOPTIMException
	This method runs the actual evaluation of the fitness, whether that is run internally (i.e., within this instance of the JAVA VM), or delegated to an external child process. More...

Protected Attributes
DGraph	dGraph
	The graph representation of the entity to evaluate. More...

IAtomContainer	fitProvMol = null
	The chemical representation of the entity to evaluate. More...

Candidate	result
	The data structure holding the results of this task. More...

String	fitProvInputFile
	The file where we store the input to the fitness provider. More...

String	fitProvOutFile
	The file where we store the final output from the fitness provider. More...

String	fitProvPNGFile
	The file where we store the graphical representation of the candidate (i.e., a picture). More...

String	fitProvUIDFile = null
	The file where we store the list of unique identifiers or previously evaluated candidates. More...

boolean	fitnessIsRequired = false
	Flag specifying if a valid fitness value is required to consider the task successfully completed. More...

FitnessParameters	fitnessSettings
	Settings for the calculation of the fitness. More...

Protected Attributes inherited from denoptim.task.Task
boolean	notifyGlobalTaskManager = false
	Flag controlling whether this task is expected to notify the static task manager. More...

boolean	completed = false
	Flag about completion. More...

boolean	hasException = false
	Flag about exception. More...

String	errMsg = ""
	Error message produced by any subtask. More...

Throwable	thrownExc
	Exception thrown. More...

int	id
	A user-assigned id for this task. More...

ProcessHandler	processHandler
	Executor for external bash script. More...

File	workDir
	The file system location where we want to be placed when doing the work. More...

int	verbosity = 0
	Verbosity level. More...

final String	SEP = System.getProperty("file.separator")
	System-dependent file separator. More...

final String	NL = System.getProperty("line.separator")
	System-dependent line separator (newline) More...

Private Member Functions
boolean	runExternalFitness () throws DENOPTIMException

boolean	runInternalFitness () throws DENOPTIMException

Additional Inherited Members
Public Attributes inherited from denoptim.task.Task
Object	lock = new Object()
	Lock for addressing synchronization issues. More...

Detailed Description

Task that assesses the fitness of a given graph.

Definition at line 49 of file FitnessTask.java.

Constructor & Destructor Documentation

◆ FitnessTask()

denoptim.task.FitnessTask.FitnessTask	(	FitnessParameters	settings,
		Candidate	c
	)

Definition at line 109 of file FitnessTask.java.

References denoptim.graph.Candidate.getGraph(), and denoptim.utils.TaskUtils.getUniqueTaskIndex().

Here is the call graph for this function:

Member Function Documentation

◆ runExternalFitness()

boolean denoptim.task.FitnessTask.runExternalFitness ( ) throws DENOPTIMException

private

Returns: true if it is all good, false in case of any reason for premature returning of the results (error generated in from the external tool, rejection on the candidate).

Exceptions

DENOPTIMException
Exception

Definition at line 197 of file FitnessTask.java.

References denoptim.constants.DENOPTIMConstants.ATMPROPVERTEXID, denoptim.graph.DGraph.cleanup(), denoptim.task.FitnessTask.dGraph, denoptim.task.Task.errMsg, denoptim.task.FitnessTask.fitnessIsRequired, denoptim.task.FitnessTask.fitnessSettings, denoptim.constants.DENOPTIMConstants.FITNESSTAG, denoptim.task.FitnessTask.fitProvInputFile, denoptim.task.FitnessTask.fitProvMol, denoptim.task.FitnessTask.fitProvOutFile, denoptim.task.FitnessTask.fitProvUIDFile, denoptim.task.ProcessHandler.getErrorOutput(), denoptim.task.ProcessHandler.getExitCode(), denoptim.fitness.FitnessParameters.getExternalFitnessProvider(), denoptim.fitness.FitnessParameters.getExternalFitnessProviderInterpreter(), denoptim.programs.RunTimeParameters.getLogger(), denoptim.graph.Candidate.getName(), denoptim.task.Task.hasException, denoptim.task.Task.lock, denoptim.constants.DENOPTIMConstants.MOLERRORTAG, denoptim.task.Task.NL, denoptim.task.Task.processHandler, denoptim.io.DenoptimIO.readAllAtomContainers(), denoptim.task.FitnessTask.result, denoptim.task.ProcessHandler.runProcess(), denoptim.graph.Candidate.setChemicalRepresentation(), denoptim.graph.Candidate.setError(), denoptim.graph.Candidate.setFitness(), denoptim.graph.Candidate.setUID(), denoptim.task.Task.thrownExc, denoptim.constants.DENOPTIMConstants.UNIQUEIDTAG, denoptim.constants.DENOPTIMConstants.UNREADABLEFILEPOSTFIX, and denoptim.task.Task.workDir.

Referenced by denoptim.task.FitnessTask.runFitnessProvider().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ runFitnessProvider()

void denoptim.task.FitnessTask.runFitnessProvider ( ) throws DENOPTIMException

protected

This method runs the actual evaluation of the fitness, whether that is run internally (i.e., within this instance of the JAVA VM), or delegated to an external child process.

Returns: the object with data obtained from the fitness provider.

Exceptions

DENOPTIMException

Definition at line 126 of file FitnessTask.java.

Referenced by denoptim.ga.OffspringEvaluationTask.call(), denoptim.programs.fitnessevaluator.FitnessEvaluationTask.call(), and denoptim.combinatorial.GraphBuildingTask.sendToFitnessProvider().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ runInternalFitness()

boolean denoptim.task.FitnessTask.runInternalFitness ( ) throws DENOPTIMException

private

Returns: true if it is all good, false in case of any reason for premature returning of the results.

Exceptions

DENOPTIMException
Exception

Definition at line 400 of file FitnessTask.java.

References denoptim.task.Task.errMsg, denoptim.task.FitnessTask.fitnessSettings, denoptim.constants.DENOPTIMConstants.FITNESSTAG, denoptim.task.FitnessTask.fitProvMol, denoptim.fitness.FitnessParameters.getDescriptors(), denoptim.fitness.FitnessProvider.getFitness(), denoptim.fitness.FitnessParameters.getFitnessExpression(), denoptim.programs.RunTimeParameters.getLogger(), denoptim.graph.Candidate.getName(), denoptim.constants.DENOPTIMConstants.MOLERRORTAG, denoptim.task.Task.NL, denoptim.task.FitnessTask.result, denoptim.graph.Candidate.setError(), and denoptim.graph.Candidate.setFitness().

Referenced by denoptim.task.FitnessTask.runFitnessProvider().

Here is the call graph for this function:

Here is the caller graph for this function:

Member Data Documentation

◆ dGraph

DGraph denoptim.task.FitnessTask.dGraph

protected

The graph representation of the entity to evaluate.

Definition at line 54 of file FitnessTask.java.

Referenced by denoptim.combinatorial.GraphBuildingTask.call(), denoptim.ga.OffspringEvaluationTask.call(), denoptim.programs.fitnessevaluator.FitnessEvaluationTask.call(), denoptim.combinatorial.GraphBuildingTask.GraphBuildingTask(), denoptim.task.FitnessTask.runExternalFitness(), and denoptim.task.FitnessTask.runFitnessProvider().

◆ fitnessIsRequired

boolean denoptim.task.FitnessTask.fitnessIsRequired = false

protected

Flag specifying if a valid fitness value is required to consider the task successfully completed.

Definition at line 100 of file FitnessTask.java.

Referenced by denoptim.task.FitnessTask.runExternalFitness().

◆ fitnessSettings

FitnessParameters denoptim.task.FitnessTask.fitnessSettings

protected

Settings for the calculation of the fitness.

Definition at line 105 of file FitnessTask.java.

Referenced by denoptim.combinatorial.GraphBuildingTask.call(), denoptim.ga.OffspringEvaluationTask.call(), denoptim.programs.fitnessevaluator.FitnessEvaluationTask.call(), denoptim.task.FitnessTask.runExternalFitness(), denoptim.task.FitnessTask.runFitnessProvider(), and denoptim.task.FitnessTask.runInternalFitness().

◆ fitProvInputFile

String denoptim.task.FitnessTask.fitProvInputFile

protected

Initial value:

= "noName"

+ DENOPTIMConstants.FITFILENAMEEXTIN

The file where we store the input to the fitness provider.

Definition at line 74 of file FitnessTask.java.

Referenced by denoptim.ga.OffspringEvaluationTask.OffspringEvaluationTask(), denoptim.task.FitnessTask.runExternalFitness(), denoptim.task.FitnessTask.runFitnessProvider(), and denoptim.combinatorial.GraphBuildingTask.sendToFitnessProvider().

◆ fitProvMol

IAtomContainer denoptim.task.FitnessTask.fitProvMol = null

protected

The chemical representation of the entity to evaluate.

We do not check for consistency between this member and the graph representation. This data structure holds also lots of attributes that are not used in all subclasses extending the FitnessTask. Moreover, it will be updated once a presumably refined molecular representation is produced by a fitness provider.

Definition at line 64 of file FitnessTask.java.

Referenced by denoptim.ga.OffspringEvaluationTask.call(), denoptim.programs.fitnessevaluator.FitnessEvaluationTask.call(), denoptim.programs.fitnessevaluator.FitnessEvaluationTask.FitnessEvaluationTask(), denoptim.task.FitnessTask.runExternalFitness(), denoptim.task.FitnessTask.runFitnessProvider(), denoptim.task.FitnessTask.runInternalFitness(), and denoptim.combinatorial.GraphBuildingTask.sendToFitnessProvider().

◆ fitProvOutFile

String denoptim.task.FitnessTask.fitProvOutFile

protected

Initial value:

= "noName"

+ DENOPTIMConstants.FITFILENAMEEXTOUT

The file where we store the final output from the fitness provider.

Definition at line 80 of file FitnessTask.java.

Referenced by denoptim.programs.fitnessevaluator.FitnessEvaluationTask.FitnessEvaluationTask(), denoptim.ga.OffspringEvaluationTask.OffspringEvaluationTask(), denoptim.task.FitnessTask.runExternalFitness(), denoptim.task.FitnessTask.runFitnessProvider(), and denoptim.combinatorial.GraphBuildingTask.sendToFitnessProvider().

◆ fitProvPNGFile

String denoptim.task.FitnessTask.fitProvPNGFile

protected

Initial value:

= "noName"

+ DENOPTIMConstants.CANDIDATE2DEXTENSION

The file where we store the graphical representation of the candidate (i.e., a picture).

Definition at line 87 of file FitnessTask.java.

Referenced by denoptim.ga.OffspringEvaluationTask.OffspringEvaluationTask(), denoptim.task.FitnessTask.runFitnessProvider(), and denoptim.combinatorial.GraphBuildingTask.sendToFitnessProvider().

◆ fitProvUIDFile

String denoptim.task.FitnessTask.fitProvUIDFile = null

protected

The file where we store the list of unique identifiers or previously evaluated candidates.

Definition at line 94 of file FitnessTask.java.

Referenced by denoptim.ga.OffspringEvaluationTask.OffspringEvaluationTask(), denoptim.task.FitnessTask.runExternalFitness(), and denoptim.combinatorial.GraphBuildingTask.sendToFitnessProvider().

◆ result

Candidate denoptim.task.FitnessTask.result

protected

The data structure holding the results of this task.

Definition at line 69 of file FitnessTask.java.

Referenced by denoptim.combinatorial.GraphBuildingTask.call(), denoptim.ga.OffspringEvaluationTask.call(), denoptim.programs.fitnessevaluator.FitnessEvaluationTask.call(), denoptim.ga.OffspringEvaluationTask.OffspringEvaluationTask(), denoptim.task.FitnessTask.runExternalFitness(), denoptim.task.FitnessTask.runFitnessProvider(), denoptim.task.FitnessTask.runInternalFitness(), and denoptim.combinatorial.GraphBuildingTask.sendToFitnessProvider().

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

/github/workspace/src/main/java/denoptim/task/FitnessTask.java

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ FitnessTask()

Member Function Documentation

◆ runExternalFitness()

◆ runFitnessProvider()

◆ runInternalFitness()

Member Data Documentation

◆ dGraph

◆ fitnessIsRequired

◆ fitnessSettings

◆ fitProvInputFile

◆ fitProvMol

◆ fitProvOutFile

◆ fitProvPNGFile

◆ fitProvUIDFile

◆ result