denoptim.programs.denovo.GAParameters Member List

This is the complete list of members for denoptim.programs.denovo.GAParameters, including all inherited members.

buildAnewFailureTolerant	denoptim.programs.denovo.GAParameters
builtAnewWeight	denoptim.programs.denovo.GAParameters	protected
checkOtherParameters()	denoptim.programs.RunTimeParameters	protected
checkParameters()	denoptim.programs.denovo.GAParameters
containsParameters(ParametersType type)	denoptim.programs.RunTimeParameters
convertProbabilityScheme(String option)	denoptim.programs.denovo.GAParameters	static
coupleMutationAndCrossover	denoptim.programs.denovo.GAParameters	protected
coupleMutationAndCrossover()	denoptim.programs.denovo.GAParameters
createWorkingDirectory()	denoptim.programs.denovo.GAParameters	private
crossoverWeight	denoptim.programs.denovo.GAParameters	protected
crowdingMultiplier	denoptim.programs.denovo.GAParameters	protected
crowdingProbabilityScheme	denoptim.programs.denovo.GAParameters	protected
crowdingSigmaMiddle	denoptim.programs.denovo.GAParameters	protected
crowdingSigmaSteepness	denoptim.programs.denovo.GAParameters	protected
dataDir	denoptim.programs.denovo.GAParameters	private
DEFUIDFILEOUTNAME	denoptim.programs.denovo.GAParameters	private
dumpMonitor	denoptim.programs.denovo.GAParameters	protected
dumpMonitor()	denoptim.programs.denovo.GAParameters
ensureFileExists(String pathname)	denoptim.programs.RunTimeParameters	protected
ensureFileExistsIfSet(String pathname)	denoptim.programs.RunTimeParameters	protected
ensureInRange(String paramName, int value, int min, int max, String paramKey)	denoptim.programs.RunTimeParameters	protected
ensureIsPositive(String paramName, int value, String paramKey)	denoptim.programs.RunTimeParameters	protected
ensureIsPositiveOrZero(String paramName, int value, String paramKey)	denoptim.programs.RunTimeParameters	protected
ensureNotNull(String paramName, String param, String paramKey)	denoptim.programs.RunTimeParameters	protected
excludedMutationTypes	denoptim.programs.denovo.GAParameters	package
GAParameters()	denoptim.programs.denovo.GAParameters
getConstructionWeight()	denoptim.programs.denovo.GAParameters
getCrossoverWeight()	denoptim.programs.denovo.GAParameters
getCrowdingFactorMiddleSigma()	denoptim.programs.denovo.GAParameters
getCrowdingFactorSteepSigma()	denoptim.programs.denovo.GAParameters
getCrowdingMultiplier()	denoptim.programs.denovo.GAParameters
getCrowdingProbabilityScheme()	denoptim.programs.denovo.GAParameters
getDataDirectory()	denoptim.programs.denovo.GAParameters
getExcludedMutationTypes()	denoptim.programs.denovo.GAParameters
getGrowthFactorMiddleSigma()	denoptim.programs.denovo.GAParameters
getGrowthFactorSteepSigma()	denoptim.programs.denovo.GAParameters
getGrowthMultiplier()	denoptim.programs.denovo.GAParameters
getGrowthProbabilityScheme()	denoptim.programs.denovo.GAParameters
getInitialPopulationFile()	denoptim.programs.denovo.GAParameters
getInitMolsToFragmentFile()	denoptim.programs.denovo.GAParameters
getInstanceFor(ParametersType paramType)	denoptim.programs.RunTimeParameters	privatestatic
getInterfaceDir()	denoptim.programs.denovo.GAParameters
getLogFilePathname()	denoptim.programs.RunTimeParameters
getLogger()	denoptim.programs.RunTimeParameters
getMaxGeneticOpAttempts()	denoptim.programs.denovo.GAParameters
getMaxRingsAddedByMutation()	denoptim.programs.denovo.GAParameters
getMaxTriesFactor()	denoptim.programs.denovo.GAParameters
getMinFitnessSD()	denoptim.programs.denovo.GAParameters
getMolGrowthFactorMiddleSigma()	denoptim.programs.denovo.GAParameters
getMolGrowthFactorSteepSigma()	denoptim.programs.denovo.GAParameters
getMolGrowthMultiplier()	denoptim.programs.denovo.GAParameters
getMolGrowthProbabilityScheme()	denoptim.programs.denovo.GAParameters
getMonitorDumpStep()	denoptim.programs.denovo.GAParameters
getMonitorFile()	denoptim.programs.denovo.GAParameters
getMultiSiteMutationWeights()	denoptim.programs.denovo.GAParameters
getMutationWeight()	denoptim.programs.denovo.GAParameters
getNumberOfChildren()	denoptim.programs.denovo.GAParameters
getNumberOfConvergenceGenerations()	denoptim.programs.denovo.GAParameters
getNumberOfCPU()	denoptim.programs.denovo.GAParameters
getNumberOfGenerations()	denoptim.programs.denovo.GAParameters
getParallelizationScheme()	denoptim.programs.denovo.GAParameters
getParameters(ParametersType type)	denoptim.programs.RunTimeParameters
getPopulationSize()	denoptim.programs.denovo.GAParameters
getPrecisionLevel()	denoptim.programs.denovo.GAParameters
getPrintedList()	denoptim.programs.denovo.GAParameters
getRandomizer()	denoptim.programs.RunTimeParameters
getRandomSeed()	denoptim.programs.RunTimeParameters
getReplacementStrategy()	denoptim.programs.denovo.GAParameters
getSaveRingSystemsAsTemplatesNonScaff()	denoptim.programs.denovo.GAParameters
getSaveRingSystemsAsTemplatesScaff()	denoptim.programs.denovo.GAParameters
getSaveRingSystemsFitnessThreshold()	denoptim.programs.denovo.GAParameters
getSelectionStrategy()	denoptim.programs.denovo.GAParameters
getSelectionStrategyType()	denoptim.programs.denovo.GAParameters
getSymmetryProbability()	denoptim.programs.denovo.GAParameters
getUIDFileIn()	denoptim.programs.denovo.GAParameters
getUIDFileOut()	denoptim.programs.denovo.GAParameters
getVerbosity()	denoptim.programs.RunTimeParameters
getVisitedGraphsFile()	denoptim.programs.denovo.GAParameters
getWorkDirectory()	denoptim.programs.RunTimeParameters
initMolsToFragmentFile	denoptim.programs.denovo.GAParameters	protected
initPoplnFile	denoptim.programs.denovo.GAParameters	protected
interfaceDir	denoptim.programs.denovo.GAParameters	private
interpretKeyword(String key, String value)	denoptim.programs.denovo.GAParameters
denoptim::programs::RunTimeParameters.interpretKeyword(String line)	denoptim.programs.RunTimeParameters
isMaster	denoptim.programs.RunTimeParameters	protected
isSortOrderDecreasing()	denoptim.programs.denovo.GAParameters
keepBestSibling	denoptim.programs.denovo.GAParameters	protected
keepBestSibling()	denoptim.programs.denovo.GAParameters
logFile	denoptim.programs.RunTimeParameters	protected
logger	denoptim.programs.RunTimeParameters	private
lvlGrowthMultiplier	denoptim.programs.denovo.GAParameters	protected
lvlGrowthProbabilityScheme	denoptim.programs.denovo.GAParameters	protected
lvlGrowthSigmaMiddle	denoptim.programs.denovo.GAParameters	protected
lvlGrowthSigmaSteepness	denoptim.programs.denovo.GAParameters	protected
maxGeneticOpAttempts	denoptim.programs.denovo.GAParameters	protected
maxOffsprintFromXover	denoptim.programs.denovo.GAParameters	protected
maxOffsprintFromXover()	denoptim.programs.denovo.GAParameters
maxRingsAddedByMutation	denoptim.programs.denovo.GAParameters	protected
maxTriesPerPop	denoptim.programs.denovo.GAParameters	protected
maxUIDMemory	denoptim.programs.denovo.GAParameters
maxXOverableSubGraphSize	denoptim.programs.denovo.GAParameters
minFitnessSD	denoptim.programs.denovo.GAParameters	protected
molGrowthMultiplier	denoptim.programs.denovo.GAParameters	protected
molGrowthProbabilityScheme	denoptim.programs.denovo.GAParameters	protected
molGrowthSigmaMiddle	denoptim.programs.denovo.GAParameters	protected
molGrowthSigmaSteepness	denoptim.programs.denovo.GAParameters	protected
monitorDumpStep	denoptim.programs.denovo.GAParameters	protected
monitorFile	denoptim.programs.denovo.GAParameters	private
mutatedGraphFailedEvalTolerant	denoptim.programs.denovo.GAParameters
mutationFailureTolerant	denoptim.programs.denovo.GAParameters
mutationWeight	denoptim.programs.denovo.GAParameters	protected
mutliSiteMutationWeights	denoptim.programs.denovo.GAParameters	private
NL	denoptim.programs.RunTimeParameters
numConvGen	denoptim.programs.denovo.GAParameters	protected
numGenerations	denoptim.programs.denovo.GAParameters	protected
numOfChildren	denoptim.programs.denovo.GAParameters	protected
numParallelTasks	denoptim.programs.denovo.GAParameters	protected
otherParameters	denoptim.programs.RunTimeParameters	protected
parallelizationScheme	denoptim.programs.denovo.GAParameters	protected
paramType	denoptim.programs.RunTimeParameters	private
paramTypeName()	denoptim.programs.RunTimeParameters
parentsSurvive	denoptim.programs.denovo.GAParameters	protected
parentsSurvive()	denoptim.programs.denovo.GAParameters
populationSize	denoptim.programs.denovo.GAParameters	protected
precisionLevel	denoptim.programs.denovo.GAParameters	protected
printParameters()	denoptim.programs.RunTimeParameters
processOtherParameters()	denoptim.programs.RunTimeParameters	protected
processParameters()	denoptim.programs.denovo.GAParameters
readParameterFile(String infile)	denoptim.programs.RunTimeParameters
readParameterLine(String line)	denoptim.programs.RunTimeParameters
readYesNoTrueFalse(String s)	denoptim.programs.RunTimeParameters	static
replacementStrategy	denoptim.programs.denovo.GAParameters	protected
rng	denoptim.programs.RunTimeParameters	private
RunTimeParameters(ParametersType paramType)	denoptim.programs.RunTimeParameters
savePopFile()	denoptim.programs.denovo.GAParameters
saveRingSystemsAsTemplatesNonScaff	denoptim.programs.denovo.GAParameters	protected
saveRingSystemsAsTemplatesScaffolds	denoptim.programs.denovo.GAParameters	protected
saveRingSystemsFitnessThreshold	denoptim.programs.denovo.GAParameters	protected
seed	denoptim.programs.denovo.GAParameters	protected
setLogFilePathname(String pathname)	denoptim.programs.RunTimeParameters
setLogger(Logger logger)	denoptim.programs.RunTimeParameters	private
setParameters(RunTimeParameters otherParams)	denoptim.programs.RunTimeParameters
setPopulationSize(int size)	denoptim.programs.denovo.GAParameters
setRandomizer(Randomizer rng)	denoptim.programs.RunTimeParameters
setVerbosity(int l)	denoptim.programs.RunTimeParameters
setWorkDirectory(String pathname)	denoptim.programs.RunTimeParameters
setWorkingDirectory(String pathName)	denoptim.programs.denovo.GAParameters
sortOrderDecreasing	denoptim.programs.denovo.GAParameters	protected
startConsoleLogger(String loggerIdentifier)	denoptim.programs.RunTimeParameters
startProgramSpecificLogger(String loggerIdentifier)	denoptim.programs.RunTimeParameters
startProgramSpecificLogger(String loggerIdentifier, boolean toLogFile)	denoptim.programs.RunTimeParameters
startRandomizer()	denoptim.programs.RunTimeParameters
startRandomizer(long seed)	denoptim.programs.RunTimeParameters
strXoverSelectionMode	denoptim.programs.denovo.GAParameters	protected
symmetricSubProbability	denoptim.programs.denovo.GAParameters	protected
timeStamp	denoptim.programs.denovo.GAParameters
uidFileIn	denoptim.programs.denovo.GAParameters	protected
uidFileOut	denoptim.programs.denovo.GAParameters	protected
uidMemoryOnDisk	denoptim.programs.denovo.GAParameters
useLevelBasedProb	denoptim.programs.denovo.GAParameters	protected
useLevelBasedProb()	denoptim.programs.denovo.GAParameters
useMolSizeBasedProb	denoptim.programs.denovo.GAParameters	protected
useMolSizeBasedProb()	denoptim.programs.denovo.GAParameters
verbosity	denoptim.programs.RunTimeParameters	protected
verbosityTologLevel()	denoptim.programs.RunTimeParameters	private
visitedGraphsFile	denoptim.programs.denovo.GAParameters	protected
workDir	denoptim.programs.RunTimeParameters	protected
writePopOnDisk	denoptim.programs.denovo.GAParameters	protected
xoverFailureTolerant	denoptim.programs.denovo.GAParameters
xoverGraphFailedEvalTolerant	denoptim.programs.denovo.GAParameters
xoverSelectionMode	denoptim.programs.denovo.GAParameters	protected