denoptim.combinatorial.CombinatorialExplorerByLayer Class Reference

Generates all combinators of fragments by means of asynchronous threads. More...

Collaboration diagram for denoptim.combinatorial.CombinatorialExplorerByLayer:

Public Member Functions
	CombinatorialExplorerByLayer (CEBLParameters settings)
	Constructor. More...
void	stopRun ()
	Stops all subtasks and shutdown executor. More...
void	run () throws DENOPTIMException
	Run the combinatorial exploration. More...

Package Attributes
final Map< GraphBuildingTask, Future< Object > >	submittedAndFutures
	Submitted subtasks and their futures. More...
final List< GraphBuildingTask >	submitted
	Sorted list of subtasks. More...
final ThreadPoolExecutor	tpe
	Asynchronous tasks manager. More...

Private Member Functions
boolean	subtaskHasException ()
	Looks for exceptions in the subtasks and, if any, store its reference locally to allow reporting it back from the main thread. More...
boolean	allTasksCompleted ()
	Check for completion of all subtasks. More...
void	makeCheckPoint () throws DENOPTIMException
	Identify the task preceding the earliest non-completed task and use it to create a checkpoint file. More...
int	countSubTasks ()
int	exploreCombinationsAtGivenLevel (int level) throws DENOPTIMException
	Generate graphs by exploring all combination of fragments at a given level of a growing graph. More...
DGraph	startNewGraphFromScaffold (int scafIdx) throws DENOPTIMException
void	cleanup ()
	clean all reference to submitted tasks More...

Private Attributes
int	verbosity = 0
	Verbosity level. More...
boolean	restartFromChkPt = false
	Flag indicating to restart from checkpoint file. More...
int	serFromChkRestart = 0
	Number of serialized graphs recovered from previous run database upon restart from checkpoint file. More...
int	totSubmittedTasks = 0
	Number of tasks submitted directly of by subtasks. More...
Throwable	thrownByTask
	If any, here we stores the exception returned by a subtask. More...
boolean	firstAfterRestart = false
	Flag identifying the first iteration after restart from checkpoint. More...
CEBLParameters	settings = null
	All settings controlling the tasks executed by this class. More...
FragmentSpaceParameters	fsSettings = null
	Settings and definition of the fragment space. More...

Detailed Description

Generates all combinators of fragments by means of asynchronous threads.

Combinations are produced by layer of fragments on root graphs, which can be single fragments (i.e., scaffolds) or complex graphs.

Author

Marco Foscato

Definition at line 61 of file CombinatorialExplorerByLayer.java.

Constructor & Destructor Documentation

CombinatorialExplorerByLayer()

denoptim.combinatorial.CombinatorialExplorerByLayer.CombinatorialExplorerByLayer

(

CEBLParameters

settings

)

Constructor.

Definition at line 127 of file CombinatorialExplorerByLayer.java.

References denoptim.combinatorial.CombinatorialExplorerByLayer.cleanup(), denoptim.programs.RunTimeParameters.containsParameters(), denoptim.programs.RunTimeParameters.ParametersType.FS_PARAMS, denoptim.combinatorial.CombinatorialExplorerByLayer.fsSettings, denoptim.programs.RunTimeParameters.getLogger(), denoptim.programs.combinatorial.CEBLParameters.getNumberOfCPU(), denoptim.programs.RunTimeParameters.getParameters(), denoptim.programs.RunTimeParameters.getVerbosity(), denoptim.programs.combinatorial.CEBLParameters.restartFromCheckPoint(), denoptim.combinatorial.CombinatorialExplorerByLayer.run(), denoptim.combinatorial.CombinatorialExplorerByLayer.settings, denoptim.combinatorial.CombinatorialExplorerByLayer.submitted, denoptim.combinatorial.CombinatorialExplorerByLayer.submittedAndFutures, denoptim.combinatorial.CombinatorialExplorerByLayer.tpe, and denoptim.combinatorial.CombinatorialExplorerByLayer.verbosity.

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Member Function Documentation

allTasksCompleted()

boolean denoptim.combinatorial.CombinatorialExplorerByLayer.allTasksCompleted ( )

private

Check for completion of all subtasks.

Returns

true if all subtasks are completed

Definition at line 247 of file CombinatorialExplorerByLayer.java.

References denoptim.combinatorial.CombinatorialExplorerByLayer.submitted.

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

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cleanup()

void denoptim.combinatorial.CombinatorialExplorerByLayer.cleanup ( )

private

clean all reference to submitted tasks

Definition at line 886 of file CombinatorialExplorerByLayer.java.

References denoptim.combinatorial.CombinatorialExplorerByLayer.submitted, denoptim.combinatorial.CombinatorialExplorerByLayer.submittedAndFutures, and denoptim.combinatorial.CombinatorialExplorerByLayer.tpe.

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

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countSubTasks()

int denoptim.combinatorial.CombinatorialExplorerByLayer.countSubTasks ( )

private

Returns

the number of subtasks submitted, which includes both the tasks submitted by the executor (i.e., child tasks) and any other tasks possibly submitted by such child tasks.

Definition at line 332 of file CombinatorialExplorerByLayer.java.

References denoptim.combinatorial.CombinatorialExplorerByLayer.submitted, and denoptim.combinatorial.CombinatorialExplorerByLayer.totSubmittedTasks.

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

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exploreCombinationsAtGivenLevel()

int denoptim.combinatorial.CombinatorialExplorerByLayer.exploreCombinationsAtGivenLevel ( int  level ) throws DENOPTIMException

private

Generate graphs by exploring all combination of fragments at a given level of a growing graph.

Note that in this context the 'level' is related to the initial root graph, which is considered to be level -1 no matter its size.

Parameters

level

the current relative level

Returns

the number of submitted tasks

Exceptions

DENOPTIMException

Definition at line 584 of file CombinatorialExplorerByLayer.java.

References denoptim.combinatorial.CombinatorialExplorerByLayer.cleanup(), denoptim.constants.DENOPTIMConstants.EOL, denoptim.combinatorial.CombinatorialExplorerByLayer.firstAfterRestart, denoptim.combinatorial.CombinatorialExplorerByLayer.fsSettings, denoptim.fragspace.FragsCombinationIterator.getCandidatesMap(), denoptim.programs.combinatorial.CEBLParameters.getCheckPoint(), denoptim.programs.combinatorial.CEBLParameters.getCheckPointStep(), denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), denoptim.programs.RunTimeParameters.getLogger(), denoptim.combinatorial.CEBLUtils.getNameOfStorageDir(), denoptim.combinatorial.CheckPoint.getNextIds(), denoptim.fragspace.FragsCombinationIterator.getNextIds(), denoptim.fragspace.FragsCombinationIterator.getNumGeneratedCombs(), denoptim.fragspace.FragsCombinationIterator.getNumRootAPs(), denoptim.programs.combinatorial.CEBLParameters.getRootGraphs(), denoptim.fragspace.FragsCombinationIterator.getSizesOfCandidateSets(), denoptim.fragspace.FragsCombinationIterator.getTotNumbCombs(), denoptim.utils.GraphUtils.getUniqueGraphIndex(), denoptim.programs.RunTimeParameters.getVerbosity(), denoptim.programs.RunTimeParameters.getWorkDirectory(), denoptim.fragspace.FragsCombinationIterator.hasNext(), denoptim.combinatorial.CombinatorialExplorerByLayer.makeCheckPoint(), denoptim.fragspace.FragsCombinationIterator.next(), denoptim.programs.combinatorial.CEBLParameters.prepareFilesForTests(), denoptim.io.DenoptimIO.readDENOPTIMGraphsFromJSONFile(), denoptim.combinatorial.CombinatorialExplorerByLayer.restartFromChkPt, denoptim.combinatorial.CheckPoint.serFileAlreadyUsed(), denoptim.constants.DENOPTIMConstants.SERGFILENAMEEXT, denoptim.combinatorial.GraphBuildingTask.setNextIds(), denoptim.fragspace.FragsCombinationIterator.setStartingPoint(), denoptim.combinatorial.CombinatorialExplorerByLayer.settings, denoptim.combinatorial.CombinatorialExplorerByLayer.startNewGraphFromScaffold(), denoptim.combinatorial.CombinatorialExplorerByLayer.stopRun(), denoptim.combinatorial.CEBLUtils.storeAllGraphsOfLevel(), denoptim.combinatorial.CombinatorialExplorerByLayer.submitted, denoptim.combinatorial.CombinatorialExplorerByLayer.submittedAndFutures, denoptim.combinatorial.CombinatorialExplorerByLayer.subtaskHasException(), denoptim.combinatorial.CombinatorialExplorerByLayer.thrownByTask, denoptim.combinatorial.CombinatorialExplorerByLayer.tpe, denoptim.programs.combinatorial.CEBLParameters.useGivenRoots, and denoptim.combinatorial.CombinatorialExplorerByLayer.verbosity.

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

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makeCheckPoint()

void denoptim.combinatorial.CombinatorialExplorerByLayer.makeCheckPoint ( ) throws DENOPTIMException

private

Identify the task preceding the earliest non-completed task and use it to create a checkpoint file.

Definition at line 269 of file CombinatorialExplorerByLayer.java.

References denoptim.programs.combinatorial.CEBLParameters.getCheckPoint(), denoptim.combinatorial.GraphBuildingTask.getGraphId(), denoptim.combinatorial.GraphBuildingTask.getLevel(), denoptim.combinatorial.GraphBuildingTask.getNextIds(), denoptim.combinatorial.GraphBuildingTask.getRootId(), denoptim.utils.GraphUtils.getUniqueGraphIndex(), denoptim.utils.GraphUtils.getUniqueMoleculeIndex(), denoptim.utils.GraphUtils.getUniqueVertexIndex(), denoptim.task.Task.isCompleted(), denoptim.combinatorial.CEBLUtils.serializeCheckPoint(), denoptim.combinatorial.CheckPoint.setLevel(), denoptim.combinatorial.CheckPoint.setNextIds(), denoptim.combinatorial.CheckPoint.setRootId(), denoptim.combinatorial.CheckPoint.setSafelyCompletedGraphId(), denoptim.combinatorial.CombinatorialExplorerByLayer.settings, denoptim.combinatorial.CheckPoint.setUnqGraphId(), denoptim.combinatorial.CheckPoint.setUnqMolId(), denoptim.combinatorial.CheckPoint.setUnqVrtId(), denoptim.combinatorial.CombinatorialExplorerByLayer.submitted, denoptim.combinatorial.CombinatorialExplorerByLayer.submittedAndFutures, and denoptim.combinatorial.CombinatorialExplorerByLayer.totSubmittedTasks.

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

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run()

void denoptim.combinatorial.CombinatorialExplorerByLayer.run

(

)

throws DENOPTIMException

Run the combinatorial exploration.

Definition at line 349 of file CombinatorialExplorerByLayer.java.

References denoptim.combinatorial.CombinatorialExplorerByLayer.allTasksCompleted(), denoptim.combinatorial.CombinatorialExplorerByLayer.cleanup(), denoptim.combinatorial.CombinatorialExplorerByLayer.countSubTasks(), denoptim.constants.DENOPTIMConstants.EOL, denoptim.combinatorial.CombinatorialExplorerByLayer.exploreCombinationsAtGivenLevel(), denoptim.combinatorial.CombinatorialExplorerByLayer.firstAfterRestart, denoptim.programs.combinatorial.CEBLParameters.getCheckPoint(), denoptim.combinatorial.CheckPoint.getLatestSafelyCompletedGraphId(), denoptim.combinatorial.CheckPoint.getLevel(), denoptim.programs.RunTimeParameters.getLogger(), denoptim.programs.combinatorial.CEBLParameters.getMaxLevel(), denoptim.programs.combinatorial.CEBLParameters.getMaxWait(), denoptim.combinatorial.CEBLUtils.getNameOfStorageDir(), denoptim.combinatorial.CheckPoint.getUnqGraphId(), denoptim.combinatorial.CheckPoint.getUnqMolId(), denoptim.combinatorial.CheckPoint.getUnqVrtId(), denoptim.programs.combinatorial.CEBLParameters.getWaitStep(), denoptim.utils.GraphUtils.resetUniqueGraphCounter(), denoptim.utils.GraphUtils.resetUniqueMoleculeCounter(), denoptim.utils.GraphUtils.resetUniqueVertexCounter(), denoptim.combinatorial.CombinatorialExplorerByLayer.restartFromChkPt, denoptim.combinatorial.CombinatorialExplorerByLayer.serFromChkRestart, denoptim.constants.DENOPTIMConstants.SERGFILENAMEEXT, denoptim.constants.DENOPTIMConstants.SERGFILENAMEROOT, denoptim.combinatorial.CombinatorialExplorerByLayer.settings, denoptim.combinatorial.CombinatorialExplorerByLayer.stopRun(), denoptim.combinatorial.CombinatorialExplorerByLayer.subtaskHasException(), denoptim.combinatorial.CombinatorialExplorerByLayer.thrownByTask, denoptim.combinatorial.CombinatorialExplorerByLayer.tpe, and denoptim.combinatorial.CombinatorialExplorerByLayer.verbosity.

Referenced by denoptim.combinatorial.CombinatorialExplorerByLayer.CombinatorialExplorerByLayer(), and denoptim.programs.combinatorial.FragSpaceExplorer.runProgram().

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startNewGraphFromScaffold()

DGraph denoptim.combinatorial.CombinatorialExplorerByLayer.startNewGraphFromScaffold ( int  scafIdx ) throws DENOPTIMException

private

Parameters

scafIdx

the molID (i.e., the index of the molecule in the library of scaffolds)

Returns

a graph containing only the scaffold of which the molID is given

Definition at line 863 of file CombinatorialExplorerByLayer.java.

References denoptim.graph.DGraph.addVertex(), denoptim.combinatorial.CombinatorialExplorerByLayer.fsSettings, denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), denoptim.utils.GraphUtils.getUniqueGraphIndex(), denoptim.utils.GraphUtils.getUniqueVertexIndex(), denoptim.graph.Vertex.newVertexFromLibrary(), denoptim.graph.Vertex.BBType.SCAFFOLD, denoptim.graph.DGraph.setGraphId(), and denoptim.graph.DGraph.setLocalMsg().

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

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stopRun()

void denoptim.combinatorial.CombinatorialExplorerByLayer.stopRun

(

)

Stops all subtasks and shutdown executor.

Definition at line 210 of file CombinatorialExplorerByLayer.java.

References denoptim.combinatorial.CombinatorialExplorerByLayer.cleanup(), and denoptim.combinatorial.CombinatorialExplorerByLayer.tpe.

Referenced by denoptim.combinatorial.CombinatorialExplorerByLayer.exploreCombinationsAtGivenLevel(), denoptim.programs.combinatorial.FragSpaceExplorer.handleThrowable(), and denoptim.combinatorial.CombinatorialExplorerByLayer.run().

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subtaskHasException()

boolean denoptim.combinatorial.CombinatorialExplorerByLayer.subtaskHasException ( )

private

Looks for exceptions in the subtasks and, if any, store its reference locally to allow reporting it back from the main thread.

Returns

true if any of the subtasks has thrown an exception

Definition at line 224 of file CombinatorialExplorerByLayer.java.

References denoptim.combinatorial.CombinatorialExplorerByLayer.submitted, and denoptim.combinatorial.CombinatorialExplorerByLayer.thrownByTask.

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

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Member Data Documentation

firstAfterRestart

boolean denoptim.combinatorial.CombinatorialExplorerByLayer.firstAfterRestart = false

private

Flag identifying the first iteration after restart from checkpoint.

Definition at line 108 of file CombinatorialExplorerByLayer.java.

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

fsSettings

FragmentSpaceParameters denoptim.combinatorial.CombinatorialExplorerByLayer.fsSettings = null

private

Settings and definition of the fragment space.

Definition at line 118 of file CombinatorialExplorerByLayer.java.

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

restartFromChkPt

boolean denoptim.combinatorial.CombinatorialExplorerByLayer.restartFromChkPt = false

private

Flag indicating to restart from checkpoint file.

Definition at line 87 of file CombinatorialExplorerByLayer.java.

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

serFromChkRestart

int denoptim.combinatorial.CombinatorialExplorerByLayer.serFromChkRestart = 0

private

Number of serialized graphs recovered from previous run database upon restart from checkpoint file.

Definition at line 93 of file CombinatorialExplorerByLayer.java.

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

settings

CEBLParameters denoptim.combinatorial.CombinatorialExplorerByLayer.settings = null

private

All settings controlling the tasks executed by this class.

Definition at line 113 of file CombinatorialExplorerByLayer.java.

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

submitted

final List<GraphBuildingTask> denoptim.combinatorial.CombinatorialExplorerByLayer.submitted

package

Sorted list of subtasks.

Definition at line 72 of file CombinatorialExplorerByLayer.java.

Referenced by denoptim.combinatorial.CombinatorialExplorerByLayer.allTasksCompleted(), denoptim.combinatorial.CombinatorialExplorerByLayer.cleanup(), denoptim.combinatorial.CombinatorialExplorerByLayer.CombinatorialExplorerByLayer(), denoptim.combinatorial.CombinatorialExplorerByLayer.countSubTasks(), denoptim.combinatorial.CombinatorialExplorerByLayer.exploreCombinationsAtGivenLevel(), denoptim.combinatorial.CombinatorialExplorerByLayer.makeCheckPoint(), and denoptim.combinatorial.CombinatorialExplorerByLayer.subtaskHasException().

submittedAndFutures

final Map<GraphBuildingTask,Future<Object> > denoptim.combinatorial.CombinatorialExplorerByLayer.submittedAndFutures

package

Submitted subtasks and their futures.

Definition at line 67 of file CombinatorialExplorerByLayer.java.

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

thrownByTask

Throwable denoptim.combinatorial.CombinatorialExplorerByLayer.thrownByTask

private

If any, here we stores the exception returned by a subtask.

Definition at line 103 of file CombinatorialExplorerByLayer.java.

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

totSubmittedTasks

int denoptim.combinatorial.CombinatorialExplorerByLayer.totSubmittedTasks = 0

private

Number of tasks submitted directly of by subtasks.

Definition at line 98 of file CombinatorialExplorerByLayer.java.

Referenced by denoptim.combinatorial.CombinatorialExplorerByLayer.countSubTasks(), and denoptim.combinatorial.CombinatorialExplorerByLayer.makeCheckPoint().

tpe

final ThreadPoolExecutor denoptim.combinatorial.CombinatorialExplorerByLayer.tpe

package

Asynchronous tasks manager.

Definition at line 77 of file CombinatorialExplorerByLayer.java.

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

verbosity

int denoptim.combinatorial.CombinatorialExplorerByLayer.verbosity = 0

private

Verbosity level.

Definition at line 82 of file CombinatorialExplorerByLayer.java.

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

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

• /github/workspace/src/main/java/denoptim/combinatorial/CombinatorialExplorerByLayer.java