Task that builds a graph by appending a given combination of fragments onto a given list of attachment points of a given root graph. More...

Inheritance diagram for denoptim.combinatorial.GraphBuildingTask:

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Collaboration diagram for denoptim.combinatorial.GraphBuildingTask:

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Public Member Functions
	GraphBuildingTask (CEBLParameters settings, DGraph molGraph, FragsCombination fragsToAdd, int level, String workDir, int verbosity) throws DENOPTIMException
	Constructor. More...

int	getNumberOfSubTasks ()

int	getLevel ()

ArrayList< Integer >	getNextIds ()
	Returns the set of indeces that identify the position of the the (next) combination of fragment in the space of combinations. More...

int	getGraphId ()
	Returns the graphID of the original graph or of the latest cyclic alternative. More...

int	getRootId ()
	Returns the graphID of the root graph. More...

void	setNextIds (ArrayList< Integer > nextIds) throws DENOPTIMException
	Set the set of indexes that identify the position of the the (next) combination of fragment in the space of combinations. More...

Object	call () throws Exception
	Calls the task. More...

Public Member Functions inherited from denoptim.task.FitnessTask
	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)

Private Member Functions
void	sendToFitnessProvider (Object[] res) throws Throwable

Private Attributes
int	rootId
	The graph ID of the root graph. More...

int	graphId
	GraphID: may be from the original graph or from its latest generated cyclic alternative. More...

int	level
	The active level of modification. More...

FragsCombination	fragsToAdd
	Pointer defining the active combination for this task. More...

int	nSubTasks = 0
	Number of subtasks. More...

ArrayList< Integer >	nextIds
	Vector of indexes identifying the next combination of fragments. More...

ThreeDimTreeBuilder	tb3d
	Tool for generating 3D models assembling 3D building blocks. More...

CEBLParameters	ceblSettings = null
	Collection of settings controlling the execution of the task. More...

FragmentSpace	fragSpace
	The fragment space. More...

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

Protected Member Functions inherited from denoptim.task.FitnessTask
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 inherited from denoptim.task.FitnessTask
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...

Detailed Description

Task that builds a graph by appending a given combination of fragments onto a given list of attachment points of a given root graph.

Author: Marco Foscato

Definition at line 57 of file GraphBuildingTask.java.

Constructor & Destructor Documentation

◆ GraphBuildingTask()

denoptim.combinatorial.GraphBuildingTask.GraphBuildingTask	(	CEBLParameters	settings,
		DGraph	molGraph,
		FragsCombination	fragsToAdd,
		int	level,
		String	workDir,
		int	verbosity
	)		throws DENOPTIMException

Constructor.

Definition at line 111 of file GraphBuildingTask.java.

References denoptim.task.FitnessTask.dGraph, denoptim.programs.RunTimeParameters.ParametersType.FIT_PARAMS, denoptim.combinatorial.GraphBuildingTask.fragsToAdd, denoptim.programs.RunTimeParameters.ParametersType.FS_PARAMS, denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), denoptim.graph.DGraph.getGraphId(), denoptim.programs.RunTimeParameters.getParameters(), denoptim.utils.GraphUtils.getUniqueGraphIndex(), denoptim.combinatorial.GraphBuildingTask.graphId, denoptim.combinatorial.GraphBuildingTask.level, denoptim.combinatorial.GraphBuildingTask.rootId, denoptim.graph.DGraph.setGraphId(), denoptim.task.Task.verbosity, and denoptim.task.Task.workDir.

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Member Function Documentation

◆ call()

Object denoptim.combinatorial.GraphBuildingTask.call ( ) throws Exception

Calls the task.

Definition at line 215 of file GraphBuildingTask.java.

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◆ getGraphId()

int denoptim.combinatorial.GraphBuildingTask.getGraphId ( )

Returns the graphID of the original graph or of the latest cyclic alternative.

Definition at line 178 of file GraphBuildingTask.java.

References denoptim.combinatorial.GraphBuildingTask.graphId.

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

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◆ getLevel()

int denoptim.combinatorial.GraphBuildingTask.getLevel ( )

Returns: the the level from which this graph has been generated

Definition at line 154 of file GraphBuildingTask.java.

References denoptim.combinatorial.GraphBuildingTask.level.

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

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◆ getNextIds()

ArrayList< Integer > denoptim.combinatorial.GraphBuildingTask.getNextIds ( )

Returns the set of indeces that identify the position of the the (next) combination of fragment in the space of combinations.

Definition at line 166 of file GraphBuildingTask.java.

References denoptim.combinatorial.GraphBuildingTask.nextIds.

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

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◆ getNumberOfSubTasks()

int denoptim.combinatorial.GraphBuildingTask.getNumberOfSubTasks ( )

Returns: the total number of serial subtasks performed by this task.

Definition at line 143 of file GraphBuildingTask.java.

References denoptim.combinatorial.GraphBuildingTask.nSubTasks.

◆ getRootId()

int denoptim.combinatorial.GraphBuildingTask.getRootId ( )

Returns the graphID of the root graph.

Definition at line 189 of file GraphBuildingTask.java.

References denoptim.combinatorial.GraphBuildingTask.rootId.

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

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◆ sendToFitnessProvider()

void denoptim.combinatorial.GraphBuildingTask.sendToFitnessProvider ( Object[] res ) throws Throwable

private

Parameters

res	the vector containing the results from the evaluation of the graph representation

Definition at line 472 of file GraphBuildingTask.java.

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

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◆ setNextIds()

void denoptim.combinatorial.GraphBuildingTask.setNextIds ( ArrayList< Integer > nextIds ) throws DENOPTIMException

Set the set of indexes that identify the position of the the (next) combination of fragment in the space of combinations.

Definition at line 201 of file GraphBuildingTask.java.

References denoptim.combinatorial.GraphBuildingTask.nextIds.

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

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Member Data Documentation

◆ ceblSettings

CEBLParameters denoptim.combinatorial.GraphBuildingTask.ceblSettings = null

private

Collection of settings controlling the execution of the task.

Definition at line 99 of file GraphBuildingTask.java.

Referenced by denoptim.combinatorial.GraphBuildingTask.call(), and denoptim.combinatorial.GraphBuildingTask.sendToFitnessProvider().

◆ fragSpace

FragmentSpace denoptim.combinatorial.GraphBuildingTask.fragSpace

private

The fragment space.

Definition at line 104 of file GraphBuildingTask.java.

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

◆ fragsToAdd

FragsCombination denoptim.combinatorial.GraphBuildingTask.fragsToAdd

private

Pointer defining the active combination for this task.

Definition at line 78 of file GraphBuildingTask.java.

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

◆ graphId

int denoptim.combinatorial.GraphBuildingTask.graphId

private

GraphID: may be from the original graph or from its latest generated cyclic alternative.

Definition at line 68 of file GraphBuildingTask.java.

Referenced by denoptim.combinatorial.GraphBuildingTask.call(), denoptim.combinatorial.GraphBuildingTask.getGraphId(), and denoptim.combinatorial.GraphBuildingTask.GraphBuildingTask().

◆ level

int denoptim.combinatorial.GraphBuildingTask.level

private

The active level of modification.

Definition at line 73 of file GraphBuildingTask.java.

Referenced by denoptim.combinatorial.GraphBuildingTask.call(), denoptim.combinatorial.GraphBuildingTask.getLevel(), denoptim.combinatorial.GraphBuildingTask.GraphBuildingTask(), and denoptim.combinatorial.GraphBuildingTask.sendToFitnessProvider().

◆ nextIds

ArrayList<Integer> denoptim.combinatorial.GraphBuildingTask.nextIds

private

Vector of indexes identifying the next combination of fragments.

This is used only to store info needed to make checkpoint files.

Definition at line 89 of file GraphBuildingTask.java.

Referenced by denoptim.combinatorial.GraphBuildingTask.call(), denoptim.combinatorial.GraphBuildingTask.getNextIds(), and denoptim.combinatorial.GraphBuildingTask.setNextIds().

◆ nSubTasks

int denoptim.combinatorial.GraphBuildingTask.nSubTasks = 0

private

Number of subtasks.

Definition at line 83 of file GraphBuildingTask.java.

Referenced by denoptim.combinatorial.GraphBuildingTask.call(), and denoptim.combinatorial.GraphBuildingTask.getNumberOfSubTasks().

◆ rootId

int denoptim.combinatorial.GraphBuildingTask.rootId

private

The graph ID of the root graph.

Definition at line 62 of file GraphBuildingTask.java.

Referenced by denoptim.combinatorial.GraphBuildingTask.call(), denoptim.combinatorial.GraphBuildingTask.getRootId(), and denoptim.combinatorial.GraphBuildingTask.GraphBuildingTask().

◆ tb3d

ThreeDimTreeBuilder denoptim.combinatorial.GraphBuildingTask.tb3d

private

Tool for generating 3D models assembling 3D building blocks.

Definition at line 94 of file GraphBuildingTask.java.

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

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

/github/workspace/src/main/java/denoptim/combinatorial/GraphBuildingTask.java

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ GraphBuildingTask()

Member Function Documentation

◆ call()

◆ getGraphId()

◆ getLevel()

◆ getNextIds()

◆ getNumberOfSubTasks()

◆ getRootId()

◆ sendToFitnessProvider()

◆ setNextIds()

Member Data Documentation

◆ ceblSettings

◆ fragSpace

◆ fragsToAdd

◆ graphId

◆ level

◆ nextIds

◆ nSubTasks

◆ rootId

◆ tb3d