Parameters controlling execution of GraphEditor. More...

Inheritance diagram for denoptim.programs.grapheditor.GraphEdParameters:

Collaboration diagram for denoptim.programs.grapheditor.GraphEdParameters:

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

ArrayList< GraphEdit >	getGraphEditTasks ()

ArrayList< DGraph >	getInputGraphs ()

IAtomContainer	getInpMol (int i)

String	getOutFile ()

boolean	symmetryFlag ()

FileFormat	getOutFormat ()

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

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

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

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

Protected Member Functions
void	readInputGraphs () throws DENOPTIMException

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...

Private Attributes
String	inGraphsFile = null
	File with input graphs. More...

ArrayList< DGraph >	inGraphs = new ArrayList<DGraph>()
	Input graphs. More...

ArrayList< IAtomContainer >	inMols
	Input molecular objects. More...

String	graphEditsFile = null
	File with list of edit tasks. More...

ArrayList< GraphEdit >	graphEdits
	Graph's editing tasks. More...

String	outGraphsFile = null
	File with output graphs. More...

FileFormat	outGraphsFormat = FileFormat.GRAPHSDF

boolean	symmetry = false
	Flag controlling strategy with respect to symmetry. 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 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 GraphEditor.

Author: Marco Foscato

Definition at line 44 of file GraphEdParameters.java.

Constructor & Destructor Documentation

◆ GraphEdParameters()

denoptim.programs.grapheditor.GraphEdParameters.GraphEdParameters ( )

Constructor.

Definition at line 87 of file GraphEdParameters.java.

References denoptim.programs.RunTimeParameters.ParametersType.GE_PARAMS.

Member Function Documentation

◆ checkParameters()

void denoptim.programs.grapheditor.GraphEdParameters.checkParameters ( ) throws DENOPTIMException

Evaluate consistency of input parameters.

Exceptions

DENOPTIMException

Reimplemented from denoptim.programs.RunTimeParameters.

Definition at line 242 of file GraphEdParameters.java.

References denoptim.files.FileUtils.checkExists(), denoptim.programs.RunTimeParameters.checkOtherParameters(), denoptim.programs.grapheditor.GraphEdParameters.graphEditsFile, denoptim.programs.grapheditor.GraphEdParameters.inGraphsFile, denoptim.programs.grapheditor.GraphEdParameters.outGraphsFile, and denoptim.programs.RunTimeParameters.workDir.

Referenced by denoptim.programs.grapheditor.GraphEditor.runProgram().

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◆ getGraphEditTasks()

ArrayList< GraphEdit > denoptim.programs.grapheditor.GraphEdParameters.getGraphEditTasks ( )

Definition at line 94 of file GraphEdParameters.java.

References denoptim.programs.grapheditor.GraphEdParameters.graphEdits.

Referenced by denoptim.programs.grapheditor.GraphEditor.runProgram().

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◆ getInpMol()

IAtomContainer denoptim.programs.grapheditor.GraphEdParameters.getInpMol ( int i )

Definition at line 108 of file GraphEdParameters.java.

References denoptim.programs.grapheditor.GraphEdParameters.inMols.

◆ getInputGraphs()

ArrayList< DGraph > denoptim.programs.grapheditor.GraphEdParameters.getInputGraphs ( )

Definition at line 101 of file GraphEdParameters.java.

References denoptim.programs.grapheditor.GraphEdParameters.inGraphs.

Referenced by denoptim.programs.grapheditor.GraphEditor.runProgram().

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◆ getOutFile()

String denoptim.programs.grapheditor.GraphEdParameters.getOutFile ( )

Definition at line 115 of file GraphEdParameters.java.

References denoptim.programs.grapheditor.GraphEdParameters.outGraphsFile.

Referenced by denoptim.programs.grapheditor.GraphEditor.runProgram().

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◆ getOutFormat()

FileFormat denoptim.programs.grapheditor.GraphEdParameters.getOutFormat ( )

Definition at line 129 of file GraphEdParameters.java.

References denoptim.programs.grapheditor.GraphEdParameters.outGraphsFormat.

Referenced by denoptim.programs.grapheditor.GraphEditor.runProgram().

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◆ getPrintedList()

String denoptim.programs.grapheditor.GraphEdParameters.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 210 of file GraphEdParameters.java.

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

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◆ interpretKeyword()

void denoptim.programs.grapheditor.GraphEdParameters.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 143 of file GraphEdParameters.java.

References denoptim.programs.grapheditor.GraphEdParameters.graphEditsFile, denoptim.files.FileFormat.GRAPHJSON, denoptim.files.FileFormat.GRAPHSDF, denoptim.programs.grapheditor.GraphEdParameters.inGraphsFile, denoptim.programs.RunTimeParameters.logFile, denoptim.programs.grapheditor.GraphEdParameters.outGraphsFile, denoptim.programs.grapheditor.GraphEdParameters.outGraphsFormat, denoptim.programs.grapheditor.GraphEdParameters.symmetry, denoptim.programs.RunTimeParameters.verbosity, and denoptim.programs.RunTimeParameters.workDir.

◆ processParameters()

void denoptim.programs.grapheditor.GraphEdParameters.processParameters ( ) throws DENOPTIMException

Processes all parameters and initialize related objects.

Exceptions

DENOPTIMException

Reimplemented from denoptim.programs.RunTimeParameters.

Definition at line 286 of file GraphEdParameters.java.

References denoptim.files.FileUtils.checkExists(), denoptim.programs.grapheditor.GraphEdParameters.graphEdits, denoptim.programs.grapheditor.GraphEdParameters.graphEditsFile, denoptim.programs.grapheditor.GraphEdParameters.inGraphsFile, denoptim.programs.grapheditor.GraphEdParameters.outGraphsFile, denoptim.programs.RunTimeParameters.processOtherParameters(), and denoptim.io.DenoptimIO.readDENOPTIMGraphEditFromFile().

Referenced by denoptim.programs.grapheditor.GraphEditor.runProgram().

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◆ readInputGraphs()

void denoptim.programs.grapheditor.GraphEdParameters.readInputGraphs ( ) throws DENOPTIMException

protected

Definition at line 317 of file GraphEdParameters.java.

References denoptim.logging.StaticLogger.appLogger, denoptim.programs.grapheditor.GraphEdParameters.inGraphs, denoptim.programs.grapheditor.GraphEdParameters.inGraphsFile, and denoptim.io.DenoptimIO.readDENOPTIMGraphsFromFile().

Referenced by denoptim.programs.grapheditor.GraphEditor.runProgram().

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◆ symmetryFlag()

boolean denoptim.programs.grapheditor.GraphEdParameters.symmetryFlag ( )

Definition at line 122 of file GraphEdParameters.java.

References denoptim.programs.grapheditor.GraphEdParameters.symmetry.

Referenced by denoptim.programs.grapheditor.GraphEditor.runProgram().

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Member Data Documentation

◆ graphEdits

ArrayList<GraphEdit> denoptim.programs.grapheditor.GraphEdParameters.graphEdits

private

Graph's editing tasks.

Definition at line 69 of file GraphEdParameters.java.

Referenced by denoptim.programs.grapheditor.GraphEdParameters.getGraphEditTasks(), and denoptim.programs.grapheditor.GraphEdParameters.processParameters().

◆ graphEditsFile

String denoptim.programs.grapheditor.GraphEdParameters.graphEditsFile = null

private

File with list of edit tasks.

Definition at line 64 of file GraphEdParameters.java.

Referenced by denoptim.programs.grapheditor.GraphEdParameters.checkParameters(), denoptim.programs.grapheditor.GraphEdParameters.interpretKeyword(), and denoptim.programs.grapheditor.GraphEdParameters.processParameters().

◆ inGraphs

ArrayList<DGraph> denoptim.programs.grapheditor.GraphEdParameters.inGraphs = new ArrayList<DGraph>()

private

Input graphs.

Definition at line 54 of file GraphEdParameters.java.

Referenced by denoptim.programs.grapheditor.GraphEdParameters.getInputGraphs(), and denoptim.programs.grapheditor.GraphEdParameters.readInputGraphs().

◆ inGraphsFile

String denoptim.programs.grapheditor.GraphEdParameters.inGraphsFile = null

private

File with input graphs.

Definition at line 49 of file GraphEdParameters.java.

Referenced by denoptim.programs.grapheditor.GraphEdParameters.checkParameters(), denoptim.programs.grapheditor.GraphEdParameters.interpretKeyword(), denoptim.programs.grapheditor.GraphEdParameters.processParameters(), and denoptim.programs.grapheditor.GraphEdParameters.readInputGraphs().

◆ inMols

ArrayList<IAtomContainer> denoptim.programs.grapheditor.GraphEdParameters.inMols

private

Input molecular objects.

Definition at line 59 of file GraphEdParameters.java.

Referenced by denoptim.programs.grapheditor.GraphEdParameters.getInpMol().

◆ outGraphsFile

String denoptim.programs.grapheditor.GraphEdParameters.outGraphsFile = null

private

File with output graphs.

Definition at line 74 of file GraphEdParameters.java.

Referenced by denoptim.programs.grapheditor.GraphEdParameters.checkParameters(), denoptim.programs.grapheditor.GraphEdParameters.getOutFile(), denoptim.programs.grapheditor.GraphEdParameters.interpretKeyword(), and denoptim.programs.grapheditor.GraphEdParameters.processParameters().

◆ outGraphsFormat

FileFormat denoptim.programs.grapheditor.GraphEdParameters.outGraphsFormat = FileFormat.GRAPHSDF

private

Definition at line 75 of file GraphEdParameters.java.

Referenced by denoptim.programs.grapheditor.GraphEdParameters.getOutFormat(), and denoptim.programs.grapheditor.GraphEdParameters.interpretKeyword().

◆ symmetry

boolean denoptim.programs.grapheditor.GraphEdParameters.symmetry = false

private

Flag controlling strategy with respect to symmetry.

Definition at line 80 of file GraphEdParameters.java.

Referenced by denoptim.programs.grapheditor.GraphEdParameters.interpretKeyword(), and denoptim.programs.grapheditor.GraphEdParameters.symmetryFlag().

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

/github/workspace/src/main/java/denoptim/programs/grapheditor/GraphEdParameters.java

Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ GraphEdParameters()

Member Function Documentation

◆ checkParameters()

◆ getGraphEditTasks()

◆ getInpMol()

◆ getInputGraphs()

◆ getOutFile()

◆ getOutFormat()

◆ getPrintedList()

◆ interpretKeyword()

◆ processParameters()

◆ readInputGraphs()

◆ symmetryFlag()

Member Data Documentation

◆ graphEdits

◆ graphEditsFile

◆ inGraphs

◆ inGraphsFile

◆ inMols

◆ outGraphsFile

◆ outGraphsFormat

◆ symmetry