A B C D E F G H I J L M N O P Q R S T U V W Y

A

abort - Variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

abort() - Method in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

activatePreParsingProcessing - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenGlobalParameters

activeNodes - Variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

activeNodes - Variable in class org.gcube.dataanalysis.executor.job.management.RemoteJobManager

actualNumberOfNodes - Variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

addEntry(int, String, String, String, List<String>) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.MatcherInput

addEntry(int, String, String, String, double, String, String, String, String, List<String>) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.MatcherOutput

allSpeciesObservations - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

appliesToAuthorship(int) - Static method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.EVBPreprocessing

appliesToScientificName(int) - Static method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.EVBPreprocessing

AquamapsNative2050Node - Class in org.gcube.dataanalysis.executor.nodes.algorithms

AquamapsNative2050Node() - Constructor for class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsNative2050Node

AquamapsNativeNode - Class in org.gcube.dataanalysis.executor.nodes.algorithms

AquamapsNativeNode() - Constructor for class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsNativeNode

AquamapsSuitable2050Node - Class in org.gcube.dataanalysis.executor.nodes.algorithms

AquamapsSuitable2050Node() - Constructor for class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitable2050Node

AquamapsSuitableFunctions - Class in org.gcube.dataanalysis.executor.nodes.algorithms

AquamapsSuitableFunctions(AquamapsAlgorithmCore, String, AlgorithmConfiguration) - Constructor for class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

AquamapsSuitableNode - Class in org.gcube.dataanalysis.executor.nodes.algorithms

AquamapsSuitableNode() - Constructor for class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode

AquamapsSuitableNode1v - Class in org.gcube.dataanalysis.executor.nodes.algorithms

AquamapsSuitableNode1v() - Constructor for class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode1v

ATTRIBUTE - Enum in org.gcube.dataanalysis.executor.messagequeue

B

BionymBiodiv - Class in org.gcube.dataanalysis.executor.nodes.transducers.bionym

BionymBiodiv() - Constructor for class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymBiodiv

BionymFlexibleWorkflowTransducer - Class in org.gcube.dataanalysis.executor.nodes.transducers.bionym

BionymFlexibleWorkflowTransducer() - Constructor for class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer

BionymLocalTransducer - Class in org.gcube.dataanalysis.executor.nodes.transducers.bionym

BionymLocalTransducer() - Constructor for class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymLocalTransducer

BiOnymWF - Class in org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.workflows

BiOnymWF(String, int, HashMap<String, String>) - Constructor for class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.workflows.BiOnymWF

BionymWorkflow - Class in org.gcube.dataanalysis.executor.nodes.transducers.bionym

BionymWorkflow() - Constructor for class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymWorkflow

broadcastTimePeriod - Static variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

buildMatcherList(AlgorithmConfiguration, String, HashMap<String, String>) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymBiodiv

buildMatcherList(AlgorithmConfiguration, String, HashMap<String, String>) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer

buildScriptFile(String, String, String, String) - Method in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent

C

calcProb(Object, Object) - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

calculateBoundingBox(Object[]) - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

callYasmeen(String) - Static method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenFileTools

closeSession() - Method in class org.gcube.dataanalysis.executor.messagequeue.Consumer

closeSession() - Method in class org.gcube.dataanalysis.executor.messagequeue.Producer

closeSession() - Method in class org.gcube.dataanalysis.executor.messagequeue.QueueManager

cometMatch(String, String, String, String, String, float, int) - Static method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.CometMatcherManager

CometMatcherManager - Class in org.gcube.dataanalysis.executor.nodes.transducers.bionym

CometMatcherManager() - Constructor for class org.gcube.dataanalysis.executor.nodes.transducers.bionym.CometMatcherManager

CometMatcherManager.Parsers - Enum in org.gcube.dataanalysis.executor.nodes.transducers.bionym

CometMatcherManager.Reference - Enum in org.gcube.dataanalysis.executor.nodes.transducers.bionym

CometMatcherManager.Weights - Enum in org.gcube.dataanalysis.executor.nodes.transducers.bionym

cometParse(String, String, String, String) - Static method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.CometMatcherManager

completeDistribution - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

computationWatcherTimerPeriod - Static variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

compute() - Method in class org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing

compute() - Method in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent

compute() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymLocalTransducer

computingNodes - Variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

config - Variable in class org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing

configurationFile - Variable in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent

connection - Variable in class org.gcube.dataanalysis.executor.messagequeue.QueueManager

connectionFactory - Variable in class org.gcube.dataanalysis.executor.messagequeue.QueueManager

consumer - Variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

Consumer - Class in org.gcube.dataanalysis.executor.messagequeue

Consumer(QueueManager, MessageListener, ExceptionListener, String) - Constructor for class org.gcube.dataanalysis.executor.messagequeue.Consumer

consumer - Variable in class org.gcube.dataanalysis.executor.messagequeue.Consumer

containerFolder - Variable in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent

contains(String, String, String, String) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.MatcherOutput

core - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

core - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode

core - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode1v

count - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.LWR

countAll - Static variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

countAllSpeciesQuery - Static variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

countCellsQuery - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode

countCellsQuery - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode1v

countCsquareCodeQuery - Static variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

countSpeciesQuery - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode

countSpeciesQuery - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode1v

createAndConnect(String, String, String, String) - Method in class org.gcube.dataanalysis.executor.messagequeue.QueueManager

createPerformanceMap() - Static method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.YasmeenMatcher

createReferenceMap() - Static method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.YasmeenMatcher

createTableStatement - Static variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

createTableStatement - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode

createTableStatement - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode1v

csquareCodeQuery - Static variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

currentconfig - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

currentconfig - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode

currentconfig - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode1v

currentconfig - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer

currentconfig - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymWorkflow

currentconfig - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.OccurrenceMergingNode

currentFAOAreas - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

currentNumberOfStages - Variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

currentSpeciesBoundingBoxInfo - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

CustomRegressor - Class in org.gcube.dataanalysis.executor.tests

CustomRegressor() - Constructor for class org.gcube.dataanalysis.executor.tests.CustomRegressor

CustomRegressor.ThreadCalculator - Class in org.gcube.dataanalysis.executor.tests

CustomRegressor.ThreadCalculator(ComputationalAgent) - Constructor for class org.gcube.dataanalysis.executor.tests.CustomRegressor.ThreadCalculator

D

D4ScienceDistributedProcessing - Class in org.gcube.dataanalysis.executor.generators

D4ScienceDistributedProcessing() - Constructor for class org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing

D4ScienceDistributedProcessing(AlgorithmConfiguration) - Constructor for class org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing

dbconnection - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer

dbconnection - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymWorkflow

dbHibConnection - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode

dbHibConnection - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode1v

dbHibConnection - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.OccurrenceMergingNode

defaultContainerFolder - Static variable in class org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing

defaultJobOutput - Static variable in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent

defaultScriptFile - Static variable in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent

deleteDuplicates - Static variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

deletefiles - Variable in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent

deleteRemoteFolder() - Method in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

destination - Variable in class org.gcube.dataanalysis.executor.messagequeue.QueueManager

destinationTable - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode

destinationTable - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode1v

destinationTable - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.LWR

destinationTableLabel - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode

destinationTableLabel - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode1v

destinationTableLabel - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.LWR

destinationTableLable - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymWorkflow

destinationTableLableParam - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer

destinationTableParam - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer

destinationTableParam - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymWorkflow

destroy() - Method in class org.gcube.dataanalysis.executor.job.management.QueueWorkerWatcher

destroy() - Method in class org.gcube.dataanalysis.executor.messagequeue.QueueManager

destroyAllWatchers() - Method in class org.gcube.dataanalysis.executor.job.management.QueueJobManager.StatusListener

distributedModel - Variable in class org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing

DistributedProcessingAgent - Class in org.gcube.dataanalysis.executor.job.management

DistributedProcessingAgent(Serializable, String, String, String, String, String, String, int, boolean, int, int) - Constructor for class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent

A distributed processing agent.

doPreprocessParam - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymWorkflow

dumpAll(String) - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

dumpCometInput(String, List<Tuple<String>>) - Static method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.CometMatcherManager

E

endpoints - Variable in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent

entries - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.MatcherInput

entries - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.MatcherOutput

environmentVectors - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

eprs - Variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

EVBPreprocessing - Class in org.gcube.dataanalysis.executor.nodes.transducers.bionym

EVBPreprocessing() - Constructor for class org.gcube.dataanalysis.executor.nodes.transducers.bionym.EVBPreprocessing

EVBPreprocessing.Preprocessors - Enum in org.gcube.dataanalysis.executor.nodes.transducers.bionym

executeBionymWorkflow(String, String, String, boolean[], float, int, float) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymWorkflow

executeChainedWorkflow(List<String>) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.GenericWorkflow

ExecuteGetLine(String, GCUBELog) - Static method in class org.gcube.dataanalysis.executor.scripts.OSCommand

executeNode(int, int, int, int, boolean, String, String, String) - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode

executeNode(int, int, int, int, boolean, String, String, String) - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode1v

executeNode(int, int, int, int, boolean, String, String, String) - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.LWR

executeNode(int, int, int, int, boolean, String, String, String) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer

executeNode(int, int, int, int, boolean, String, String, String) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymWorkflow

executeNode(int, int, int, int, boolean, String, String, String) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.OccurrenceMergingNode

executeWF(String[]) - Static method in class org.gcube.dataanalysis.executor.tests.TestBiOnym2_0_0

F

familyColumn - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.LWR

FileCopy(String, String) - Static method in class org.gcube.dataanalysis.executor.scripts.OSCommand

filenames - Variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

fileurls - Variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

filterMatchedTuples(List<Tuple<String>>) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymWorkflow

filterProbabilitySet(Queue<String>) - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode

filterProbabilitySet(Queue<String>) - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode1v

forceUpload - Static variable in class org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing

forceUpload - Variable in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent

FuzzyMatcher - Class in org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers

FuzzyMatcher(String, double, int, HashMap<String, String>) - Constructor for class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers.FuzzyMatcher

fuzzymatchorigins - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.EVBPreprocessing

fuzzymatchtargets - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.EVBPreprocessing

G

generate(AlgorithmConfiguration) - Static method in class org.gcube.dataanalysis.executor.tests.TestBiOnym1_0_0

generate(AlgorithmConfiguration) - Static method in class org.gcube.dataanalysis.executor.tests.TestBiOnym2_0_0

generate(AlgorithmConfiguration) - Static method in class org.gcube.dataanalysis.executor.tests.TestBiOnymEvaluation

generate(AlgorithmConfiguration) - Static method in class org.gcube.dataanalysis.executor.tests.TestD4ScienceMaps

generate(AlgorithmConfiguration) - Static method in class org.gcube.dataanalysis.executor.tests.TestD4ScienceQueueMaps

generate(AlgorithmConfiguration) - Static method in class org.gcube.dataanalysis.executor.tests.TestD4ScienceQueueMaps2

generate(AlgorithmConfiguration) - Static method in class org.gcube.dataanalysis.executor.tests.TestD4ScienceQueueMaps2_1

generate(AlgorithmConfiguration) - Static method in class org.gcube.dataanalysis.executor.tests.TestD4ScienceQueueMaps2_2

generate(AlgorithmConfiguration) - Static method in class org.gcube.dataanalysis.executor.tests.TestD4ScienceQueueMaps3

generate(AlgorithmConfiguration) - Static method in class org.gcube.dataanalysis.executor.tests.TestD4ScienceQueueMultipleMaps

generate(AlgorithmConfiguration) - Static method in class org.gcube.dataanalysis.executor.tests.TestGenerator

GenericWorkflow - Class in org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts

GenericWorkflow(String, HashMap<String, String>) - Constructor for class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.GenericWorkflow

getActiveNodes() - Method in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

getActiveNodes() - Method in class org.gcube.dataanalysis.executor.job.management.RemoteJobManager

getAdditionalInformation(Object, Object) - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

getAlgorithm() - Method in class org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing

getBoundingBoxInformation(Object[], Object[]) - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

getConfig() - Static method in class org.gcube.dataanalysis.executor.tests.CustomRegressor

getConfig() - Static method in class org.gcube.dataanalysis.executor.tests.RegressionTestLWR

example of parallel processing on a single machine the procedure will generate a new table for a distribution on suitable species

getDescription() - Method in class org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing

getDescription() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsNative2050Node

getDescription() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsNativeNode

getDescription() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitable2050Node

getDescription() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode

getDescription() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode1v

getDescription() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.LWR

getDescription() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymBiodiv

getDescription() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer

getDescription() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymLocalTransducer

getDescription() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymWorkflow

getDescription() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.OccurrenceMergingNode

getEntriesNumber() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.MatcherInput

getEntriesNumber() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.MatcherOutput

getEntry(int) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.MatcherInput

getEntry(int) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.MatcherOutput

getEnum2Matcher(YasmeenGlobalParameters.BuiltinMatchers, String, double, int, HashMap<String, String>) - Static method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer

getGenerationConfig(int, String, String, String, String, String, String, String, String) - Static method in class org.gcube.dataanalysis.executor.tests.TestGenerator

getGeographicalID(Object) - Static method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

getInfrastructure() - Method in class org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing

getInfrastructure() - Method in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent

getInfrastructure() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymLocalTransducer

getInputParameters() - Method in class org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing

getInputParameters() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode

getInputParameters() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode1v

getInputParameters() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.LWR

getInputParameters() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymBiodiv

getInputParameters() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer

getInputParameters() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymLocalTransducer

getInputParameters() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymWorkflow

getInputParameters() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.OccurrenceMergingNode

getInternalStatus() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode

getInternalStatus() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode1v

getInternalStatus() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.LWR

getInternalStatus() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer

getInternalStatus() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymWorkflow

getInternalStatus() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.OccurrenceMergingNode

getLexicalDistancesWeights() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.YasmeenMatcher

getLexicalDistancesWeights() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers.FuzzyMatcher

getLexicalDistancesWeights() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers.GsayMatcher

getLexicalDistancesWeights() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers.LevensteinMatcher

getLexicalDistancesWeights() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers.MixedLexicalMatcher

getLexicalDistancesWeights() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers.SoundexMatcher

getLexicalDistancesWeights() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers.TrigramMatcher

getLoad() - Method in class org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing

getLoad() - Method in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent

getMainInfoID(Object) - Static method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

getMatchersList() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.GenericWorkflow

getMatches() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.CometMatcherManager

getMatchlets() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.YasmeenMatcher

getMatchlets() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers.FuzzyMatcher

getMatchlets() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers.GsayMatcher

getMatchlets() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers.LevensteinMatcher

getMatchlets() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers.MixedLexicalMatcher

getMatchlets() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers.SoundexMatcher

getMatchlets() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers.TrigramMatcher

getName() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsNative2050Node

getName() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsNativeNode

getName() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitable2050Node

getName() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode

getName() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode1v

getName() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.LWR

getName() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymBiodiv

getName() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer

getName() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymWorkflow

getName() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.OccurrenceMergingNode

getNumberOfGeoInfo() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode1v

getNumberOfLeftElements() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode

getNumberOfLeftElements() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.LWR

getNumberOfLeftElements() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer

getNumberOfLeftElements() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymWorkflow

getNumberOfLeftElements() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.OccurrenceMergingNode

getNumberOfNodes() - Method in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

getNumberOfNodes() - Method in class org.gcube.dataanalysis.executor.job.management.RemoteJobManager

getNumberOfProcessedSpecies() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode1v

getNumberOfRightElements() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode

getNumberOfRightElements() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.LWR

getNumberOfRightElements() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer

getNumberOfRightElements() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymWorkflow

getNumberOfRightElements() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.OccurrenceMergingNode

getNumberOfSpecies() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode1v

getOutput() - Method in class org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing

getOutput() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode

getOutput() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode1v

getOutput() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.LWR

getOutput() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer

getOutput() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymLocalTransducer

getOutput() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymWorkflow

getOutput() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.OccurrenceMergingNode

getProperties() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode

getProperties() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode1v

getProperties() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.LWR

getProperties() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer

getProperties() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymWorkflow

getProperties() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.OccurrenceMergingNode

getResourceLoad() - Method in class org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing

getResourceLoad() - Method in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent

getResourceLoad() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymLocalTransducer

getResources() - Method in class org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing

getResources() - Method in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent

getResources() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymLocalTransducer

getScores() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.CometMatcherManager

getState() - Method in class org.gcube.dataanalysis.executor.job.management.WorkerWatcher

getStatus() - Method in class org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing

getStatus() - Method in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent

getStatus() - Method in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

getStatus() - Method in class org.gcube.dataanalysis.executor.job.management.RemoteJobManager

getStatus() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymLocalTransducer

getStemming() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.YasmeenMatcher

getStemming() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers.FuzzyMatcher

getStemming() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers.GsayMatcher

getStemming() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers.LevensteinMatcher

getStemming() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers.MixedLexicalMatcher

getStemming() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers.SoundexMatcher

getStemming() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers.TrigramMatcher

getString(String) - Static method in class org.gcube.dataanalysis.executor.scripts.ScriptIOWorker

getSupportedAlgorithms() - Method in class org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing

getSupportedAlgorithms() - Method in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent

getYasmeenMatcherOutput(String, String) - Static method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenFileTools

getYasmeenParserOutput(String, String) - Static method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenFileTools

globalparameters - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.GenericWorkflow

GsayMatcher - Class in org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers

GsayMatcher(String, double, int, HashMap<String, String>) - Constructor for class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers.GsayMatcher

gscope - Variable in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent

gscope - Variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

H

hasResent() - Method in class org.gcube.dataanalysis.executor.job.management.QueueWorkerWatcher

hasResentMessages() - Method in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent

hasResentMessages() - Method in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

headers - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer

I

id - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.SingleEntry

identifier - Variable in class org.gcube.dataanalysis.executor.messagequeue.Producer

init() - Method in class org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing

init(String, int) - Method in class org.gcube.dataanalysis.executor.job.management.RemoteJobManager

init(HashMap<String, String>) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.GenericWorkflow

init(String, double, int, HashMap<String, String>) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.YasmeenMatcher

init() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymLocalTransducer

init(String, HashMap<String, String>) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.parsers.YasmeenParser

init(String, double, int, HashMap<String, String>) - Method in interface org.gcube.dataanalysis.executor.nodes.transducers.bionym.interfaces.Matcher

init(String, HashMap<String, String>) - Method in interface org.gcube.dataanalysis.executor.nodes.transducers.bionym.interfaces.Parser

init(HashMap<String, String>) - Method in interface org.gcube.dataanalysis.executor.nodes.transducers.bionym.interfaces.PostProcessor

initSingleNode(AlgorithmConfiguration) - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode

initSingleNode(AlgorithmConfiguration) - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode1v

initSingleNode(AlgorithmConfiguration) - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.LWR

initSingleNode(AlgorithmConfiguration) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer

initSingleNode(AlgorithmConfiguration) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymWorkflow

initSingleNode(AlgorithmConfiguration) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.OccurrenceMergingNode

J

jobManager - Variable in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent

L

leftSetNumberOfElements - Variable in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent

LevensteinMatcher - Class in org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers

LevensteinMatcher(String, double, int, HashMap<String, String>) - Constructor for class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers.LevensteinMatcher

logger - Variable in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent

LWR - Class in org.gcube.dataanalysis.executor.nodes.algorithms

LWR() - Constructor for class org.gcube.dataanalysis.executor.nodes.algorithms.LWR

M

main(String[]) - Static method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.EVBPreprocessing

main(String[]) - Static method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.test.TestBiOnymBiodiv

main(String[]) - Static method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.test.TestBiOnymGenericWF

main(String[]) - Static method in class org.gcube.dataanalysis.executor.tests.RegressionTestGenerators

example of parallel processing on a single machine the procedure will generate a new table for a distribution on suitable species

main(String[]) - Static method in class org.gcube.dataanalysis.executor.tests.RegressionTestLWR

main(String[]) - Static method in class org.gcube.dataanalysis.executor.tests.RegressionTestTransducers

main(String[]) - Static method in class org.gcube.dataanalysis.executor.tests.TestBiOnym1_0_0

main(String[]) - Static method in class org.gcube.dataanalysis.executor.tests.TestBiOnym2_0_0

main(String[]) - Static method in class org.gcube.dataanalysis.executor.tests.TestBiOnymEvaluation

main(String[]) - Static method in class org.gcube.dataanalysis.executor.tests.TestBiOnymLocal

main(String[]) - Static method in class org.gcube.dataanalysis.executor.tests.TestD4ScienceMaps

main(String[]) - Static method in class org.gcube.dataanalysis.executor.tests.TestD4ScienceQueueMaps

main(String[]) - Static method in class org.gcube.dataanalysis.executor.tests.TestD4ScienceQueueMaps2

main(String[]) - Static method in class org.gcube.dataanalysis.executor.tests.TestD4ScienceQueueMaps2_1

main(String[]) - Static method in class org.gcube.dataanalysis.executor.tests.TestD4ScienceQueueMaps2_2

main(String[]) - Static method in class org.gcube.dataanalysis.executor.tests.TestD4ScienceQueueMaps3

main(String[]) - Static method in class org.gcube.dataanalysis.executor.tests.TestD4ScienceQueueMultipleMaps

main(String[]) - Static method in class org.gcube.dataanalysis.executor.tests.TestGetRunningExecutor

main(String[]) - Static method in class org.gcube.dataanalysis.executor.tests.TestRemoteJobLaunch

main1(String[]) - Static method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.test.TestBiOnymGenericWF

main2(String[]) - Static method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode

main2(String[]) - Static method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode1v

main2(String[]) - Static method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.test.TestBiOnymGenericWF

mainclass - Variable in class org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing

mainclass - Variable in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent

mainTEST(String[]) - Static method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymWorkflow

mainTest(String[]) - Static method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.workflows.BiOnymWF

manager - Variable in class org.gcube.dataanalysis.executor.messagequeue.Consumer

manager - Variable in class org.gcube.dataanalysis.executor.messagequeue.Producer

match(MatcherInput) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.YasmeenMatcher

match(String, String, String, List<Tuple<String>>, float, int) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.CometMatcherManager

match(MatcherInput) - Method in interface org.gcube.dataanalysis.executor.nodes.transducers.bionym.interfaces.Matcher

Matcher - Interface in org.gcube.dataanalysis.executor.nodes.transducers.bionym.interfaces

MatcherInput - Class in org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts

MatcherInput() - Constructor for class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.MatcherInput

matcherLib - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.YasmeenMatcher

MatcherOutput - Class in org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts

MatcherOutput() - Constructor for class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.MatcherOutput

matcherParam - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenGlobalParameters

matcherParamPrefix - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer

matchersList - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.GenericWorkflow

matchingScore - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.SingleEntry

maxElementsAllowedPerJob - Variable in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent

maxFailureTries - Variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

maxMatchersInterface - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer

maxMatchersReal - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer

maxMatchesParam - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymWorkflow

maxMessagesAllowedPerJob - Static variable in class org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing

maxNumberOfComputationRetries - Static variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

maxNumberOfStages - Static variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

maxResults - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.YasmeenMatcher

maxresultsParamPrefix - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer

maxSilenceTimeBeforeComputationStop - Static variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

maxwaitingTime - Variable in class org.gcube.dataanalysis.executor.job.management.QueueWorkerWatcher

mergeOutputs(List<MatcherOutput>) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.GenericWorkflow

mergeOutputs(List<MatcherOutput>) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.workflows.BiOnymWF

messagesresent - Variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

metainfo - Static variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

MixedLexicalMatcher - Class in org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers

MixedLexicalMatcher(String, double, int, HashMap<String, String>) - Constructor for class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers.MixedLexicalMatcher

modelName - Variable in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent

mqurl - Variable in class org.gcube.dataanalysis.executor.messagequeue.QueueManager

N

numberOfCells - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

numberOfMessages - Variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

numberOfSpecies - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

O

OccurrenceIntersectionNode - Class in org.gcube.dataanalysis.executor.nodes.transducers

OccurrenceIntersectionNode() - Constructor for class org.gcube.dataanalysis.executor.nodes.transducers.OccurrenceIntersectionNode

OccurrenceMergingNode - Class in org.gcube.dataanalysis.executor.nodes.transducers

OccurrenceMergingNode() - Constructor for class org.gcube.dataanalysis.executor.nodes.transducers.OccurrenceMergingNode

OccurrenceSubtractionNode - Class in org.gcube.dataanalysis.executor.nodes.transducers

OccurrenceSubtractionNode() - Constructor for class org.gcube.dataanalysis.executor.nodes.transducers.OccurrenceSubtractionNode

onException(JMSException) - Method in class org.gcube.dataanalysis.executor.job.management.QueueJobManager.StatusListener

onMessage(Message) - Method in class org.gcube.dataanalysis.executor.job.management.QueueJobManager.StatusListener

operations - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode

operations - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode1v

org.gcube.dataanalysis.executor.generators - package org.gcube.dataanalysis.executor.generators

org.gcube.dataanalysis.executor.job.management - package org.gcube.dataanalysis.executor.job.management

org.gcube.dataanalysis.executor.messagequeue - package org.gcube.dataanalysis.executor.messagequeue

org.gcube.dataanalysis.executor.nodes.algorithms - package org.gcube.dataanalysis.executor.nodes.algorithms

org.gcube.dataanalysis.executor.nodes.transducers - package org.gcube.dataanalysis.executor.nodes.transducers

org.gcube.dataanalysis.executor.nodes.transducers.bionym - package org.gcube.dataanalysis.executor.nodes.transducers.bionym

org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts - package org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts

org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers - package org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers

org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.parsers - package org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.parsers

org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.workflows - package org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.workflows

org.gcube.dataanalysis.executor.nodes.transducers.bionym.interfaces - package org.gcube.dataanalysis.executor.nodes.transducers.bionym.interfaces

org.gcube.dataanalysis.executor.nodes.transducers.bionym.test - package org.gcube.dataanalysis.executor.nodes.transducers.bionym.test

org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils - package org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils

org.gcube.dataanalysis.executor.scripts - package org.gcube.dataanalysis.executor.scripts

org.gcube.dataanalysis.executor.tests - package org.gcube.dataanalysis.executor.tests

originalName - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.SingleEntry

originTable - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.LWR

originTableParam - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer

originTableParam - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymWorkflow

OSCommand - Class in org.gcube.dataanalysis.executor.scripts

OSCommand() - Constructor for class org.gcube.dataanalysis.executor.scripts.OSCommand

otherElements - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.SingleEntry

outputmap - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymLocalTransducer

overallMaxResults - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenGlobalParameters

P

parameters - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.YasmeenMatcher

parameters - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.parsers.YasmeenParser

parse(List<String>) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.parsers.YasmeenParser

parse(List<String>) - Method in interface org.gcube.dataanalysis.executor.nodes.transducers.bionym.interfaces.Parser

parseCometOutput(String) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.CometMatcherManager

parseCometParserOutput(String) - Static method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.CometMatcherManager

parsedAuthorship - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.SingleEntry

parsedScientificName - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.SingleEntry

parser - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.GenericWorkflow

Parser - Interface in org.gcube.dataanalysis.executor.nodes.transducers.bionym.interfaces

parserInputFileParam - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenGlobalParameters

parserLib - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.parsers.YasmeenParser

parserNameParam - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenGlobalParameters

parserOutputFileParam - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenGlobalParameters

parserParam - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymWorkflow

pathToLib - Variable in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent

performanceParam - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenGlobalParameters

populateTuples(List<String>) - Static method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.EVBPreprocessing

postparsecleaning - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.EVBPreprocessing

postparsecleaningorigin - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.EVBPreprocessing

postparsecleaningtargets - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.EVBPreprocessing

postProcess(boolean, boolean) - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode

postProcess(boolean, boolean) - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode1v

postProcess(boolean, boolean) - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.LWR

postProcess(boolean, boolean) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer

postProcess(boolean, boolean) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymWorkflow

postProcess(boolean, boolean) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.OccurrenceMergingNode

postProcess1(boolean) - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode1v

postProcess2(boolean) - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode1v

postProcess4(boolean) - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode1v

postprocessMatches(MatcherOutput) - Method in interface org.gcube.dataanalysis.executor.nodes.transducers.bionym.interfaces.PostProcessor

postprocessor - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.GenericWorkflow

PostProcessor - Interface in org.gcube.dataanalysis.executor.nodes.transducers.bionym.interfaces

preparsecleaning - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.EVBPreprocessing

preparsecleaningorigins - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.EVBPreprocessing

preparsecleaningtargets - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.EVBPreprocessing

preprocess(String, String, List<String>) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.EVBPreprocessing

prevbroadcastTimePeriod - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.LWR

prevbroadcastTimePeriod - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer

prevbroadcastTimePeriod - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymWorkflow

prevbroadcastTimePeriod - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.OccurrenceMergingNode

prevmaxMessages - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.LWR

prevmaxMessages - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer

prevmaxMessages - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymWorkflow

prevmaxMessages - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.OccurrenceMergingNode

prevmaxNumberOfStages - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.LWR

prevmaxNumberOfStages - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer

prevmaxNumberOfStages - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymWorkflow

prevmaxNumberOfStages - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.OccurrenceMergingNode

probabilityInsertionStatement - Static variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

process(ComputationalAgent) - Static method in class org.gcube.dataanalysis.executor.tests.CustomRegressor

processedAreas - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

produce(String) - Static method in class org.gcube.dataanalysis.executor.tests.TestD4ScienceQueueMaps

produceAnalytics() - Method in interface org.gcube.dataanalysis.executor.nodes.transducers.bionym.interfaces.PostProcessor

producer - Variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

Producer - Class in org.gcube.dataanalysis.executor.messagequeue

Producer(QueueManager, String) - Constructor for class org.gcube.dataanalysis.executor.messagequeue.Producer

producer - Variable in class org.gcube.dataanalysis.executor.messagequeue.Producer

pruningThresholdParam - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymWorkflow

purgeQueues() - Method in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

Q

QCONSTANTS - Class in org.gcube.dataanalysis.executor.messagequeue

QCONSTANTS() - Constructor for class org.gcube.dataanalysis.executor.messagequeue.QCONSTANTS

QueueJobManager - Class in org.gcube.dataanalysis.executor.job.management

QueueJobManager(String, int) - Constructor for class org.gcube.dataanalysis.executor.job.management.QueueJobManager

QueueJobManager(String, int, List<EndpointReferenceType>) - Constructor for class org.gcube.dataanalysis.executor.job.management.QueueJobManager

QueueJobManager.Broadcaster - Class in org.gcube.dataanalysis.executor.job.management

QueueJobManager.Broadcaster() - Constructor for class org.gcube.dataanalysis.executor.job.management.QueueJobManager.Broadcaster

QueueJobManager.ComputationTimerWatcher - Class in org.gcube.dataanalysis.executor.job.management

QueueJobManager.ComputationTimerWatcher(long) - Constructor for class org.gcube.dataanalysis.executor.job.management.QueueJobManager.ComputationTimerWatcher

QueueJobManager.StatusListener - Class in org.gcube.dataanalysis.executor.job.management

QueueJobManager.StatusListener() - Constructor for class org.gcube.dataanalysis.executor.job.management.QueueJobManager.StatusListener

QueueLifeTime - Static variable in class org.gcube.dataanalysis.executor.messagequeue.QCONSTANTS

QueueManager - Class in org.gcube.dataanalysis.executor.messagequeue

QueueManager() - Constructor for class org.gcube.dataanalysis.executor.messagequeue.QueueManager

queueName - Variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

queuePWD - Variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

queueResponse - Variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

queueURL - Variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

queueUSER - Variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

queueWatcherMaxwaitingTime - Static variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

QueueWorkerWatcher - Class in org.gcube.dataanalysis.executor.job.management

QueueWorkerWatcher(Producer, Map<String, Object>, int) - Constructor for class org.gcube.dataanalysis.executor.job.management.QueueWorkerWatcher

R

rawnamesColumnParam - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer

rawnamesColumnParam - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymWorkflow

rawnamescount - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer

rebuildAll(int, int, int, int, String) - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

rebuildConfig(String) - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

referenceParam - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymWorkflow

refreshStatusTime - Static variable in class org.gcube.dataanalysis.executor.messagequeue.QCONSTANTS

RegressionTestGenerators - Class in org.gcube.dataanalysis.executor.tests

RegressionTestGenerators() - Constructor for class org.gcube.dataanalysis.executor.tests.RegressionTestGenerators

RegressionTestLWR - Class in org.gcube.dataanalysis.executor.tests

RegressionTestLWR() - Constructor for class org.gcube.dataanalysis.executor.tests.RegressionTestLWR

RegressionTestTransducers - Class in org.gcube.dataanalysis.executor.tests

RegressionTestTransducers() - Constructor for class org.gcube.dataanalysis.executor.tests.RegressionTestTransducers

RemoteJobManager - Class in org.gcube.dataanalysis.executor.job.management

RemoteJobManager(String, int) - Constructor for class org.gcube.dataanalysis.executor.job.management.RemoteJobManager

RemoteJobManager(String, int, List<EndpointReferenceType>) - Constructor for class org.gcube.dataanalysis.executor.job.management.RemoteJobManager

resent - Variable in class org.gcube.dataanalysis.executor.job.management.QueueWorkerWatcher

resentMessages - Variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

reset() - Method in class org.gcube.dataanalysis.executor.job.management.QueueJobManager.ComputationTimerWatcher

resetMatchers(List<Matcher>) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.GenericWorkflow

resetTime() - Method in class org.gcube.dataanalysis.executor.job.management.QueueWorkerWatcher

rightSetNumberOfElements - Variable in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent

run() - Method in class org.gcube.dataanalysis.executor.job.management.QueueJobManager.Broadcaster

run() - Method in class org.gcube.dataanalysis.executor.job.management.QueueJobManager.ComputationTimerWatcher

run() - Method in class org.gcube.dataanalysis.executor.tests.CustomRegressor.ThreadCalculator

run() - Method in class org.gcube.dataanalysis.executor.tests.TestD4ScienceQueueMaps.ThreadGenerator

run() - Method in class org.gcube.dataanalysis.executor.tests.TestD4ScienceQueueMultipleMaps.ThreadGenerator

run() - Method in class org.gcube.dataanalysis.executor.tests.TestGenerator

S

sandboxFolder - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.GenericWorkflow

sandBoxFolder - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.YasmeenMatcher

sandboxFolder - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.parsers.YasmeenParser

scope - Variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

ScriptIOWorker - Class in org.gcube.dataanalysis.executor.scripts

ScriptIOWorker() - Constructor for class org.gcube.dataanalysis.executor.scripts.ScriptIOWorker

selectAllSpeciesObservationQuery - Static variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

selectAllSpeciesQuery - Static variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

sendMessage(Object, long) - Method in class org.gcube.dataanalysis.executor.messagequeue.Producer

sendTextMessage(String, long) - Method in class org.gcube.dataanalysis.executor.messagequeue.Producer

session - Variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

session - Variable in class org.gcube.dataanalysis.executor.messagequeue.QueueManager

setConfiguration(AlgorithmConfiguration) - Method in class org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing

setConfiguration(AlgorithmConfiguration) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymLocalTransducer

setEndPoints(List<String>) - Method in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent

setLogger(Logger) - Method in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent

setmaxTime(long) - Method in class org.gcube.dataanalysis.executor.job.management.QueueJobManager.ComputationTimerWatcher

setNumberOfNodes(int) - Method in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

setNumberOfNodes(int) - Method in class org.gcube.dataanalysis.executor.job.management.RemoteJobManager

setup(AlgorithmConfiguration) - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode

setup(AlgorithmConfiguration) - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode1v

setup(AlgorithmConfiguration) - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.LWR

setup(AlgorithmConfiguration) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer

setup(AlgorithmConfiguration) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymWorkflow

setup(AlgorithmConfiguration) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.OccurrenceMergingNode

shutdown() - Method in class org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing

shutdown() - Method in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent

shutdown - Variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

shutdown() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymLocalTransducer

SingleEntry - Class in org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts

SingleEntry(int, String, String, String, double, String, String, String, String, List<String>) - Constructor for class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.SingleEntry

SingleEntry(int, String, String, String, List<String>) - Constructor for class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.SingleEntry

singleStepPostprocess(Object) - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsNativeNode

singleStepPostprocess(Object) - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode

singleStepPostprocess(Object) - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode1v

singleStepPreprocess(Object, boolean) - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode

singleStepPreprocess(Object, boolean) - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode1v

SoundexMatcher - Class in org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers

SoundexMatcher(String, double, int, HashMap<String, String>) - Constructor for class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers.SoundexMatcher

soundexweightParam - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymWorkflow

speciesName - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymLocalTransducer

speciesVectors - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

standBy() - Method in class org.gcube.dataanalysis.executor.messagequeue.Consumer

standBy() - Method in class org.gcube.dataanalysis.executor.messagequeue.Producer

status - Variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

status - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.LWR

status - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymLocalTransducer

stop - Variable in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent

stop() - Method in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

stop() - Method in class org.gcube.dataanalysis.executor.job.management.RemoteJobManager

stop() - Method in class org.gcube.dataanalysis.executor.messagequeue.Consumer

stop() - Method in class org.gcube.dataanalysis.executor.messagequeue.Producer

stop() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode

stop() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode1v

stop() - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.LWR

stop() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer

stop() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymWorkflow

stop() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.OccurrenceMergingNode

subdivisiondiv - Variable in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent

T

targetAuthor - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.SingleEntry

targetDataSource - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.SingleEntry

targetID - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.SingleEntry

targetScientificName - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.SingleEntry

taxaAuthorityFileParam - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenGlobalParameters

TestBiOnym1_0_0 - Class in org.gcube.dataanalysis.executor.tests

TestBiOnym1_0_0() - Constructor for class org.gcube.dataanalysis.executor.tests.TestBiOnym1_0_0

TestBiOnym2_0_0 - Class in org.gcube.dataanalysis.executor.tests

TestBiOnym2_0_0() - Constructor for class org.gcube.dataanalysis.executor.tests.TestBiOnym2_0_0

TestBiOnymBiodiv - Class in org.gcube.dataanalysis.executor.nodes.transducers.bionym.test

TestBiOnymBiodiv() - Constructor for class org.gcube.dataanalysis.executor.nodes.transducers.bionym.test.TestBiOnymBiodiv

TestBiOnymEvaluation - Class in org.gcube.dataanalysis.executor.tests

TestBiOnymEvaluation() - Constructor for class org.gcube.dataanalysis.executor.tests.TestBiOnymEvaluation

TestBiOnymGenericWF - Class in org.gcube.dataanalysis.executor.nodes.transducers.bionym.test

TestBiOnymGenericWF() - Constructor for class org.gcube.dataanalysis.executor.nodes.transducers.bionym.test.TestBiOnymGenericWF

TestBiOnymLocal - Class in org.gcube.dataanalysis.executor.tests

TestBiOnymLocal() - Constructor for class org.gcube.dataanalysis.executor.tests.TestBiOnymLocal

TestD4ScienceMaps - Class in org.gcube.dataanalysis.executor.tests

TestD4ScienceMaps() - Constructor for class org.gcube.dataanalysis.executor.tests.TestD4ScienceMaps

TestD4ScienceQueueMaps - Class in org.gcube.dataanalysis.executor.tests

TestD4ScienceQueueMaps() - Constructor for class org.gcube.dataanalysis.executor.tests.TestD4ScienceQueueMaps

TestD4ScienceQueueMaps.ThreadGenerator - Class in org.gcube.dataanalysis.executor.tests

TestD4ScienceQueueMaps.ThreadGenerator(String) - Constructor for class org.gcube.dataanalysis.executor.tests.TestD4ScienceQueueMaps.ThreadGenerator

TestD4ScienceQueueMaps2 - Class in org.gcube.dataanalysis.executor.tests

TestD4ScienceQueueMaps2() - Constructor for class org.gcube.dataanalysis.executor.tests.TestD4ScienceQueueMaps2

TestD4ScienceQueueMaps2_1 - Class in org.gcube.dataanalysis.executor.tests

TestD4ScienceQueueMaps2_1() - Constructor for class org.gcube.dataanalysis.executor.tests.TestD4ScienceQueueMaps2_1

TestD4ScienceQueueMaps2_2 - Class in org.gcube.dataanalysis.executor.tests

TestD4ScienceQueueMaps2_2() - Constructor for class org.gcube.dataanalysis.executor.tests.TestD4ScienceQueueMaps2_2

TestD4ScienceQueueMaps3 - Class in org.gcube.dataanalysis.executor.tests

TestD4ScienceQueueMaps3() - Constructor for class org.gcube.dataanalysis.executor.tests.TestD4ScienceQueueMaps3

TestD4ScienceQueueMultipleMaps - Class in org.gcube.dataanalysis.executor.tests

TestD4ScienceQueueMultipleMaps() - Constructor for class org.gcube.dataanalysis.executor.tests.TestD4ScienceQueueMultipleMaps

TestD4ScienceQueueMultipleMaps.ThreadGenerator - Class in org.gcube.dataanalysis.executor.tests

TestD4ScienceQueueMultipleMaps.ThreadGenerator(AlgorithmConfiguration) - Constructor for class org.gcube.dataanalysis.executor.tests.TestD4ScienceQueueMultipleMaps.ThreadGenerator

TestGenerator - Class in org.gcube.dataanalysis.executor.tests

TestGenerator(ComputationalAgent) - Constructor for class org.gcube.dataanalysis.executor.tests.TestGenerator

TestGetRunningExecutor - Class in org.gcube.dataanalysis.executor.tests

TestGetRunningExecutor() - Constructor for class org.gcube.dataanalysis.executor.tests.TestGetRunningExecutor

TestRemoteJobLaunch - Class in org.gcube.dataanalysis.executor.tests

TestRemoteJobLaunch() - Constructor for class org.gcube.dataanalysis.executor.tests.TestRemoteJobLaunch

threshold - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.YasmeenMatcher

thresholdParamPrefix - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer

timeToLive - Static variable in class org.gcube.dataanalysis.executor.messagequeue.QCONSTANTS

toInputString(String) - Static method in class org.gcube.dataanalysis.executor.scripts.ScriptIOWorker

topic - Variable in class org.gcube.dataanalysis.executor.messagequeue.Producer

toString() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.SingleEntry

totalNumberOfMessages - Variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

totalNumberOfStages - Variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

TrigramMatcher - Class in org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers

TrigramMatcher(String, double, int, HashMap<String, String>) - Constructor for class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers.TrigramMatcher

type - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

type - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode

type - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode1v

U

uploadAndExecute(String, String, String, String, String, String, String, List<String>, boolean) - Method in class org.gcube.dataanalysis.executor.job.management.RemoteJobManager

uploadAndExecuteChunkized(String, String, String, String, String, String, String, List<String>, String, boolean, boolean) - Method in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

userName - Variable in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent

useStemmedGenusAndSpecies - Static variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenGlobalParameters

V

valueOf(String) - Static method in enum org.gcube.dataanalysis.executor.messagequeue.ATTRIBUTE

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.gcube.dataanalysis.executor.nodes.transducers.bionym.CometMatcherManager.Parsers

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.gcube.dataanalysis.executor.nodes.transducers.bionym.CometMatcherManager.Reference

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.gcube.dataanalysis.executor.nodes.transducers.bionym.CometMatcherManager.Weights

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.gcube.dataanalysis.executor.nodes.transducers.bionym.EVBPreprocessing.Preprocessors

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenGlobalParameters.BuiltinDataSources

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenGlobalParameters.BuiltinMatchers

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenGlobalParameters.BuiltinParsers

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenGlobalParameters.Performance

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.gcube.dataanalysis.executor.messagequeue.ATTRIBUTE

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.gcube.dataanalysis.executor.nodes.transducers.bionym.CometMatcherManager.Parsers

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.gcube.dataanalysis.executor.nodes.transducers.bionym.CometMatcherManager.Reference

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.gcube.dataanalysis.executor.nodes.transducers.bionym.CometMatcherManager.Weights

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.gcube.dataanalysis.executor.nodes.transducers.bionym.EVBPreprocessing.Preprocessors

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenGlobalParameters.BuiltinDataSources

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenGlobalParameters.BuiltinMatchers

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenGlobalParameters.BuiltinParsers

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenGlobalParameters.Performance

Returns an array containing the constants of this enum type, in the order they are declared.

W

waitForMessages() - Method in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

wake() - Method in class org.gcube.dataanalysis.executor.messagequeue.Consumer

wake() - Method in class org.gcube.dataanalysis.executor.messagequeue.Producer

wasAborted() - Method in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

wasAborted() - Method in class org.gcube.dataanalysis.executor.job.management.RemoteJobManager

WorkerWatcher - Class in org.gcube.dataanalysis.executor.job.management

WorkerWatcher(TaskProxy, Logger) - Constructor for class org.gcube.dataanalysis.executor.job.management.WorkerWatcher

writeOnDB(List<String>, String, SessionFactory) - Static method in class org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableFunctions

writeYasmeenMatcherInput(String, String, String, MatcherInput) - Static method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenFileTools

Deprecated.

writeYasmeenParserInput(String, String, List<String>) - Static method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenFileTools

Y

YasmeenFileTools - Class in org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils

YasmeenFileTools() - Constructor for class org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenFileTools

YasmeenGlobalParameters - Class in org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils

YasmeenGlobalParameters() - Constructor for class org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenGlobalParameters

YasmeenGlobalParameters.BuiltinDataSources - Enum in org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils

YasmeenGlobalParameters.BuiltinMatchers - Enum in org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils

YasmeenGlobalParameters.BuiltinParsers - Enum in org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils

YasmeenGlobalParameters.Performance - Enum in org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils

YasmeenMatcher - Class in org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts

YasmeenMatcher(String, double, int, HashMap<String, String>) - Constructor for class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.YasmeenMatcher

YasmeenParser - Class in org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.parsers

YasmeenParser() - Constructor for class org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.parsers.YasmeenParser

yetstopped - Variable in class org.gcube.dataanalysis.executor.job.management.QueueJobManager

A B C D E F G H I J L M N O P Q R S T U V W Y