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

A

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

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

agePlusGroupInp - Static variable in class org.gcube.dataanalysis.executor.nodes.algorithms.ICCATVPA

AlgorithmClassParameter - Static variable in class org.gcube.dataanalysis.executor.job.management.GenericWorker

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

analyseContent(String, String) - Method in class org.gcube.dataanalysis.executor.rscripts.generic.GenericRScript

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

assembleFiles(String) - Method in class org.gcube.dataanalysis.executor.nodes.algorithms.FAOMSY

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

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

byteCountToDisplaySize(BigInteger) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Returns a human-readable version of the file size, where the input represents a specific number of bytes.

byteCountToDisplaySize(long) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Returns a human-readable version of the file size, where the input represents a specific number of bytes.

C

CAAInp - Static variable in class org.gcube.dataanalysis.executor.nodes.algorithms.ICCATVPA

CAAInpURL - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.ICCATVPA

calcFileRows(File, boolean) - Static method in class org.gcube.dataanalysis.executor.util.StorageUtils

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

callTask(boolean) - Method in class org.gcube.dataanalysis.executor.job.management.WPSJobManager.TasksWatcher

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

checksum(File, Checksum) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Computes the checksum of a file using the specified checksum object.

checksumCRC32(File) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Computes the checksum of a file using the CRC32 checksum routine.

cleanDirectory(File) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Cleans a directory without deleting it.

close(URLConnection) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Closes a URLConnection.

closeQuietly(Reader) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Unconditionally close an Reader.

closeQuietly(Writer) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Unconditionally close a Writer.

closeQuietly(InputStream) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Unconditionally close an InputStream.

closeQuietly(OutputStream) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Unconditionally close an OutputStream.

closeQuietly(Closeable) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Unconditionally close a Closeable.

closeQuietly(Socket) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Unconditionally close a Socket.

closeQuietly(Selector) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Unconditionally close a Selector.

closeQuietly(ServerSocket) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Unconditionally close a ServerSocket.

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

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

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

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

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

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

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

concat(String, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Concatenates a filename to a base path using normal command line style rules.

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

config - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.ICCATVPA

configuration - Variable in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgentWPS

ConfigurationFileParameter - Static variable in class org.gcube.dataanalysis.executor.job.management.GenericWorker

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

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

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.DistributedProcessingAgentWPS

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

contentEquals(File, File) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Compares the contents of two files to determine if they are equal or not.

contentEquals(InputStream, InputStream) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Compare the contents of two Streams to determine if they are equal or not.

contentEquals(Reader, Reader) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Compare the contents of two Readers to determine if they are equal or not.

contentEqualsIgnoreEOL(File, File, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Compares the contents of two files to determine if they are equal or not.

contentEqualsIgnoreEOL(Reader, Reader) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Compare the contents of two Readers to determine if they are equal or not, ignoring EOL characters.

convertFileCollectionToFileArray(Collection<File>) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Converts a Collection containing java.io.File instanced into array representation.

copy(InputStream, OutputStream) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Copy bytes from an InputStream to an OutputStream.

copy(InputStream, Writer) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Copy bytes from an InputStream to chars on a Writer using the default character encoding of the platform.

copy(InputStream, Writer, Charset) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Copy bytes from an InputStream to chars on a Writer using the specified character encoding.

copy(InputStream, Writer, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Copy bytes from an InputStream to chars on a Writer using the specified character encoding.

copy(Reader, Writer) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Copy chars from a Reader to a Writer.

copy(Reader, OutputStream) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Copy chars from a Reader to bytes on an OutputStream using the default character encoding of the platform, and calling flush.

copy(Reader, OutputStream, Charset) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Copy chars from a Reader to bytes on an OutputStream using the specified character encoding, and calling flush.

copy(Reader, OutputStream, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Copy chars from a Reader to bytes on an OutputStream using the specified character encoding, and calling flush.

copyDirectory(File, File) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Copies a whole directory to a new location preserving the file dates.

copyDirectory(File, File, boolean) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Copies a whole directory to a new location.

copyDirectory(File, File, FileFilter) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Copies a filtered directory to a new location preserving the file dates.

copyDirectory(File, File, FileFilter, boolean) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Copies a filtered directory to a new location.

copyDirectoryToDirectory(File, File) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Copies a directory to within another directory preserving the file dates.

copyFile(File, File) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Copies a file to a new location preserving the file date.

copyFile(File, File, boolean) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Copies a file to a new location.

copyFile(File, OutputStream) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Copy bytes from a File to an OutputStream.

copyFileToDirectory(File, File) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Copies a file to a directory preserving the file date.

copyFileToDirectory(File, File, boolean) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Copies a file to a directory optionally preserving the file date.

copyInputStreamToFile(InputStream, File) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Copies bytes from an InputStream source to a file destination.

copyLarge(InputStream, OutputStream) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Copy bytes from a large (over 2GB) InputStream to an OutputStream.

copyLarge(InputStream, OutputStream, byte[]) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Copy bytes from a large (over 2GB) InputStream to an OutputStream.

copyLarge(InputStream, OutputStream, long, long) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Copy some or all bytes from a large (over 2GB) InputStream to an OutputStream, optionally skipping input bytes.

copyLarge(InputStream, OutputStream, long, long, byte[]) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Copy some or all bytes from a large (over 2GB) InputStream to an OutputStream, optionally skipping input bytes.

copyLarge(Reader, Writer) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Copy chars from a large (over 2GB) Reader to a Writer.

copyLarge(Reader, Writer, char[]) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Copy chars from a large (over 2GB) Reader to a Writer.

copyLarge(Reader, Writer, long, long) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Copy some or all chars from a large (over 2GB) InputStream to an OutputStream, optionally skipping input chars.

copyLarge(Reader, Writer, long, long, char[]) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Copy some or all chars from a large (over 2GB) InputStream to an OutputStream, optionally skipping input chars.

copyURLToFile(URL, File) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Copies bytes from the URL source to a file destination.

copyURLToFile(URL, File, int, int) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Copies bytes from the URL source to a file destination.

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.CMSY

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

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

CPUEcutInp - Static variable in class org.gcube.dataanalysis.executor.nodes.algorithms.ICCATVPA

CPUEInp - Static variable in class org.gcube.dataanalysis.executor.nodes.algorithms.ICCATVPA

CPUEInpURL - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.ICCATVPA

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

createReferenceMapFile(String) - 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

currentFolder - Variable in class org.gcube.dataanalysis.executor.rscripts.generic.GenericRScript

currentOutputFileName - Variable in class org.gcube.dataanalysis.executor.util.LocalRScriptsManager

currentOutputFileName - Variable in class org.gcube.dataanalysis.executor.util.RScriptsManager

currentOutputURL - Variable in class org.gcube.dataanalysis.executor.util.LocalRScriptsManager

currentOutputURL - Variable in class org.gcube.dataanalysis.executor.util.RScriptsManager

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

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

DataTransferer - Class in org.gcube.dataanalysis.executor.util

DataTransferer() - Constructor for class org.gcube.dataanalysis.executor.util.DataTransferer

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.DistributedProcessingAgentWPS

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

deleteDirectory(File) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Deletes a directory recursively.

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

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

deleteQuietly(File) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Deletes a file, never throwing an exception.

DeleteTemporaryFilesParameter - Static variable in class org.gcube.dataanalysis.executor.job.management.GenericWorker

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.messagequeue.QueueManager

DIR_SEPARATOR - Static variable in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

The system directory separator character.

DIR_SEPARATOR_UNIX - Static variable in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

The Unix directory separator character.

DIR_SEPARATOR_WINDOWS - Static variable in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

The Windows directory separator character.

directoryContains(String, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Determines whether the parent directory contains the child element (a file or directory).

directoryContains(File, File) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Determines whether the parent directory contains the child element (a file or directory).

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

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

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

A distributed processing agent.

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

downloadFilefromStorage(String, String, String, String) - Static method in class org.gcube.dataanalysis.executor.util.StorageUtils

downloadInputFile(String, String) - Static method in class org.gcube.dataanalysis.executor.util.StorageUtils

downloadInputFile(String, String, boolean) - Static method in class org.gcube.dataanalysis.executor.util.StorageUtils

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

effectInp - Static variable in class org.gcube.dataanalysis.executor.nodes.algorithms.ICCATVPA

EMPTY_FILE_ARRAY - Static variable in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

An empty array of type File.

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

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

environmentalvariables - Variable in class org.gcube.dataanalysis.executor.rscripts.generic.GenericRScript

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

equals(String, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Checks whether two filenames are equal exactly.

equals(String, String, boolean, IOCase) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Checks whether two filenames are equal, optionally normalizing and providing control over the case-sensitivity.

equalsNormalized(String, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Checks whether two filenames are equal after both have been normalized.

equalsNormalizedOnSystem(String, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Checks whether two filenames are equal after both have been normalized and using the case rules of the system.

equalsOnSystem(String, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Checks whether two filenames are equal using the case rules of the system.

estimateNumberOfServices(String) - Method in class org.gcube.dataanalysis.executor.job.management.WPSJobManager

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

executeAlgorithm(String, int, int, int, int, boolean, String, File, boolean) - Method in class org.gcube.dataanalysis.executor.job.management.GenericWorker

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, Logger) - 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.CMSY

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

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

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

executeRScript(AlgorithmConfiguration, String, String, HashMap<String, String>, String, String, HashMap<String, String>, boolean, boolean, String) - Method in class org.gcube.dataanalysis.executor.util.LocalRScriptsManager

executeRScript(AlgorithmConfiguration, String, String, HashMap<String, String>, HashMap<String, String>, String, String, HashMap<String, String>, boolean, boolean, String) - Method in class org.gcube.dataanalysis.executor.util.LocalRScriptsManager

executeRScript(AlgorithmConfiguration, String, String, HashMap<String, String>, String, String, HashMap<String, String>, boolean, boolean, boolean, String) - Method in class org.gcube.dataanalysis.executor.util.LocalRScriptsManager

executeRScript(AlgorithmConfiguration, String, String, HashMap<String, String>, HashMap<String, String>, String, String, HashMap<String, String>, boolean, boolean, boolean, String) - Method in class org.gcube.dataanalysis.executor.util.LocalRScriptsManager

executeRScript(AlgorithmConfiguration, String, String, HashMap<String, String>, String, String, HashMap<String, String>, boolean, boolean, String) - Method in class org.gcube.dataanalysis.executor.util.RScriptsManager

executeRScript(AlgorithmConfiguration, String, String, HashMap<String, String>, String, String, HashMap<String, String>, boolean, boolean, boolean, String) - Method in class org.gcube.dataanalysis.executor.util.RScriptsManager

exitstatus - Variable in class org.gcube.dataanalysis.executor.job.management.WPSJobManager.TasksWatcher

EXTENSION_SEPARATOR - Static variable in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

The extension separator character.

EXTENSION_SEPARATOR_STR - Static variable in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

The extension separator String.

F

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

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

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

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

FilenameUtils - Class in org.gcube.dataanalysis.executor.rscripts.generic

General filename and filepath manipulation utilities.

FilenameUtils() - Constructor for class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Instances should NOT be constructed in standard programming.

FileSubset(File, File, int, int, boolean) - Static method in class org.gcube.dataanalysis.executor.util.StorageUtils

FileUtils - Class in org.gcube.dataanalysis.executor.rscripts.generic

General file manipulation utilities.

FileUtils() - Constructor for class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Instances should NOT be constructed in standard programming.

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

findEmailingSystemAddress(String) - Static method in class org.gcube.dataanalysis.executor.util.InfraRetrieval

forceDelete(File) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Deletes a file.

forceDeleteOnExit(File) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Schedules a file to be deleted when JVM exits.

forceMkdir(File) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Makes a directory, including any necessary but nonexistent parent directories.

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

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

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

generateRemoteLogFile(String) - Method in class org.gcube.dataanalysis.executor.rscripts.generic.GenericRScript

GenericRScript - Class in org.gcube.dataanalysis.executor.rscripts.generic

GenericRScript() - Constructor for class org.gcube.dataanalysis.executor.rscripts.generic.GenericRScript

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

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

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

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

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.WPSJobManager

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

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

getBaseName(String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Gets the base name, minus the full path and extension, from a full filename.

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

getCallTemplate() - Static method in class org.gcube.dataanalysis.executor.job.management.WPSJobManager

getCurrentOutputFileName() - Method in class org.gcube.dataanalysis.executor.util.LocalRScriptsManager

getCurrentOutputFileName() - Method in class org.gcube.dataanalysis.executor.util.RScriptsManager

getCurrentOutputURL() - Method in class org.gcube.dataanalysis.executor.util.LocalRScriptsManager

getCurrentOutputURL() - Method in class org.gcube.dataanalysis.executor.util.RScriptsManager

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

getDescription() - Method in class org.gcube.dataanalysis.executor.job.management.GenericWorker

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.CMSY

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

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

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

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

getDescription() - Method in class org.gcube.dataanalysis.executor.rscripts.KnitrCompiler

getDescription() - Method in class org.gcube.dataanalysis.executor.rscripts.SGVMS_Interpolation

getDescription() - Method in class org.gcube.dataanalysis.executor.rscripts.TemplateRScripts

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

getExtension(String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Gets the extension of a filename.

getFile(File, String...) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Construct a file from the set of name elements.

getFile(String...) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Construct a file from the set of name elements.

getFullPath(String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Gets the full path from a full filename, which is the prefix + path.

getFullPathNoEndSeparator(String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Gets the full path from a full filename, which is the prefix + path, and also excluding the final directory separator.

getGenericWorkerCall(String, String, AlgorithmConfiguration, int, int, int, int, boolean, boolean, String) - Static method in class org.gcube.dataanalysis.executor.job.management.GenericWorkerCaller

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.DistributedProcessingAgentWPS

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.CMSY

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

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

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.CMSY

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

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

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.DistributedProcessingAgentWPS

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.CMSY

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

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

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

getName(String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Gets the name minus the path from a full filename.

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.CMSY

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

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

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.WPSJobManager

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.CMSY

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

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

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.CMSY

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

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

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

getOutput() - Method in class org.gcube.dataanalysis.executor.rscripts.generic.GenericRScript

getOutput() - Method in class org.gcube.dataanalysis.executor.rscripts.KnitrCompiler

getOutput() - Method in class org.gcube.dataanalysis.executor.rscripts.SGVMS_Interpolation

getOutput() - Method in class org.gcube.dataanalysis.executor.rscripts.TemplateRScripts

getPath(String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Gets the path from a full filename, which excludes the prefix.

getPathNoEndSeparator(String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Gets the path from a full filename, which excludes the prefix, and also excluding the final directory separator.

getPrefix(String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Gets the prefix from a full filename, such as C:/ or ~/.

getPrefixLength(String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Returns the length of the filename prefix, such as C:/ or ~/.

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.CMSY

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

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

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.DistributedProcessingAgentWPS

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.DistributedProcessingAgentWPS

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

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

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

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

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

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

getStatus() - Method in class org.gcube.dataanalysis.executor.rscripts.generic.GenericRScript

getStatus() - Method in class org.gcube.dataanalysis.executor.util.LocalRScriptsManager

getStatus() - Method in class org.gcube.dataanalysis.executor.util.RScriptsManager

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.DistributedProcessingAgentWPS

getTempDirectory() - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Returns a File representing the system temporary directory.

getTempDirectoryPath() - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Returns the path to the system temporary directory.

getTransferInfo(String) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.WebApplicationPublisher

getUserDirectory() - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Returns a File representing the user's home directory.

getUserDirectoryPath() - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Returns the path to the user's home directory.

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.DistributedProcessingAgentWPS

H

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

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

hasResentTrue() - Method in class org.gcube.dataanalysis.executor.job.management.WPSJobManager

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

I

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

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

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

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

incrementOverallFailures() - Method in class org.gcube.dataanalysis.executor.job.management.WPSJobManager

incrementOverallSuccess() - Method in class org.gcube.dataanalysis.executor.job.management.WPSJobManager

indexOfExtension(String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Returns the index of the last extension separator character, which is a dot.

indexOfLastSeparator(String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Returns the index of the last directory separator character.

InfraRetrieval - Class in org.gcube.dataanalysis.executor.util

InfraRetrieval() - Constructor for class org.gcube.dataanalysis.executor.util.InfraRetrieval

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

init() - Method in class org.gcube.dataanalysis.executor.job.management.GenericWorker

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

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

init() - Method in class org.gcube.dataanalysis.executor.rscripts.generic.GenericRScript

init() - Method in class org.gcube.dataanalysis.executor.rscripts.SGVMS_Interpolation

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.CMSY

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

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

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

initVariables() - Method in class org.gcube.dataanalysis.executor.rscripts.generic.GenericRScript

initVariables() - Method in class org.gcube.dataanalysis.executor.rscripts.KnitrCompiler

initVariables() - Method in class org.gcube.dataanalysis.executor.rscripts.TemplateRScripts

INPUT_DATA - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.RealTimeMatcher

INPUT_DATA_ID - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.RealTimeMatcher

INPUT_DATA_SOURCE_ID - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.RealTimeMatcher

inputStreamToFile(InputStream, String) - Static method in class org.gcube.dataanalysis.executor.util.StorageUtils

inputvariables - Variable in class org.gcube.dataanalysis.executor.rscripts.generic.GenericRScript

IOUtils - Class in org.gcube.dataanalysis.executor.rscripts.generic

General IO stream manipulation utilities.

IOUtils() - Constructor for class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Instances should NOT be constructed in standard programming.

IsDuplicateParameter - Static variable in class org.gcube.dataanalysis.executor.job.management.GenericWorker

isExtension(String, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Checks whether the extension of the filename is that specified.

isExtension(String, String[]) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Checks whether the extension of the filename is one of those specified.

isExtension(String, Collection<String>) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Checks whether the extension of the filename is one of those specified.

isFileNewer(File, File) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Tests if the specified File is newer than the reference File.

isFileNewer(File, Date) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Tests if the specified File is newer than the specified Date.

isFileNewer(File, long) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Tests if the specified File is newer than the specified time reference.

isFileOlder(File, File) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Tests if the specified File is older than the reference File.

isFileOlder(File, Date) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Tests if the specified File is older than the specified Date.

isFileOlder(File, long) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Tests if the specified File is older than the specified time reference.

isStopped() - Method in class org.gcube.dataanalysis.executor.job.management.WPSJobManager

isSymlink(File) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Determines whether the specified file is a Symbolic Link rather than an actual file.

iterateFiles(File, IOFileFilter, IOFileFilter) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Allows iteration over the files in given directory (and optionally its subdirectories).

iterateFiles(File, String[], boolean) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Allows iteration over the files in a given directory (and optionally its subdirectories) which match an array of extensions.

iterateFilesAndDirs(File, IOFileFilter, IOFileFilter) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Allows iteration over the files in given directory (and optionally its subdirectories).

J

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

K

KnitrCompiler - Class in org.gcube.dataanalysis.executor.rscripts

KnitrCompiler() - Constructor for class org.gcube.dataanalysis.executor.rscripts.KnitrCompiler

L

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

LeftSetStartIndexParameter - Static variable in class org.gcube.dataanalysis.executor.job.management.GenericWorker

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

LINE_SEPARATOR - Static variable in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

The system line separator string.

LINE_SEPARATOR_UNIX - Static variable in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

The Unix line separator string.

LINE_SEPARATOR_WINDOWS - Static variable in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

The Windows line separator string.

lineIterator(File, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Returns an Iterator for the lines in a File.

lineIterator(File) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Returns an Iterator for the lines in a File using the default encoding for the VM.

lineIterator(Reader) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Return an Iterator for the lines in a Reader.

lineIterator(InputStream, Charset) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Return an Iterator for the lines in an InputStream, using the character encoding specified (or default encoding if null).

lineIterator(InputStream, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Return an Iterator for the lines in an InputStream, using the character encoding specified (or default encoding if null).

listFiles(File, IOFileFilter, IOFileFilter) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Finds files within a given directory (and optionally its subdirectories).

listFiles(File, String[], boolean) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Finds files within a given directory (and optionally its subdirectories) which match an array of extensions.

listFilesAndDirs(File, IOFileFilter, IOFileFilter) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Finds files within a given directory (and optionally its subdirectories).

LocalRScriptsManager - Class in org.gcube.dataanalysis.executor.util

LocalRScriptsManager() - Constructor for class org.gcube.dataanalysis.executor.util.LocalRScriptsManager

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

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.abstracts.RealTimeMatcher

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.util.RScriptsManager

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

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

main1(String[]) - Static method in class org.gcube.dataanalysis.executor.util.RScriptsManager

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.DistributedProcessingAgentWPS

mainScriptName - Variable in class org.gcube.dataanalysis.executor.rscripts.generic.GenericRScript

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(String, String, String, String, double, int) - Method in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.RealTimeMatcher

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.DistributedProcessingAgentWPS

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

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

mergeFiles(String, List<String>, String, boolean) - Static method in class org.gcube.dataanalysis.executor.util.StorageUtils

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

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.DistributedProcessingAgentWPS

moveDirectory(File, File) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Moves a directory.

moveDirectoryToDirectory(File, File, boolean) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Moves a directory to another directory.

moveFile(File, File) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Moves a file.

moveFileToDirectory(File, File, File, boolean) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

moveFileToDirectory(File, File, boolean) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Moves a file to a directory.

moveToDirectory(File, File, boolean) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Moves a file or directory to the destination directory.

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

N

nCPUEInp - Static variable in class org.gcube.dataanalysis.executor.nodes.algorithms.ICCATVPA

normalize(String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Normalizes a path, removing double and single dot path steps.

normalize(String, boolean) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Normalizes a path, removing double and single dot path steps.

normalizeNoEndSeparator(String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Normalizes a path, removing double and single dot path steps, and removing any final directory separator.

normalizeNoEndSeparator(String, boolean) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Normalizes a path, removing double and single dot path steps, and removing any final directory separator.

nRemoveYearInp - Static variable in class org.gcube.dataanalysis.executor.nodes.algorithms.ICCATVPA

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

NumberOfLeftElementsToProcessParameter - Static variable in class org.gcube.dataanalysis.executor.job.management.GenericWorker

NumberOfRightElementsToProcessParameter - Static variable in class org.gcube.dataanalysis.executor.job.management.GenericWorker

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

ONE_EB - Static variable in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

The number of bytes in an exabyte.

ONE_EB_BI - Static variable in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

The number of bytes in an exabyte.

ONE_GB - Static variable in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

The number of bytes in a gigabyte.

ONE_GB_BI - Static variable in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

The number of bytes in a gigabyte.

ONE_KB - Static variable in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

The number of bytes in a kilobyte.

ONE_KB_BI - Static variable in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

The number of bytes in a kilobyte.

ONE_MB - Static variable in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

The number of bytes in a megabyte.

ONE_MB_BI - Static variable in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

The number of bytes in a megabyte.

ONE_PB - Static variable in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

The number of bytes in a petabyte.

ONE_PB_BI - Static variable in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

The number of bytes in a petabyte.

ONE_TB - Static variable in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

The number of bytes in a terabyte.

ONE_TB_BI - Static variable in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

The number of bytes in a terabyte.

ONE_YB - Static variable in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

The number of bytes in a yottabyte.

ONE_ZB - Static variable in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

The number of bytes in a zettabyte.

openInputStream(File) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Opens a FileInputStream for the specified file, providing better error messages than simply calling new FileInputStream(file).

openOutputStream(File) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Opens a FileOutputStream for the specified file, checking and creating the parent directory if it does not exist.

openOutputStream(File, boolean) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Opens a FileOutputStream for the specified file, checking and creating the parent directory if it does not exist.

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.ecoengine.interfaces - package org.gcube.dataanalysis.ecoengine.interfaces

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.rscripts - package org.gcube.dataanalysis.executor.rscripts

org.gcube.dataanalysis.executor.rscripts.generic - package org.gcube.dataanalysis.executor.rscripts.generic

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

org.gcube.dataanalysis.executor.util - package org.gcube.dataanalysis.executor.util

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

output - Variable in class org.gcube.dataanalysis.executor.rscripts.generic.GenericRScript

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

OutputParameter - Static variable in class org.gcube.dataanalysis.executor.job.management.GenericWorker

outputValues - Variable in class org.gcube.dataanalysis.executor.rscripts.generic.GenericRScript

outputvariables - Variable in class org.gcube.dataanalysis.executor.rscripts.generic.GenericRScript

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

P

packageURL - Static variable in class org.gcube.dataanalysis.executor.nodes.algorithms.ICCATVPA

packageURL - Variable in class org.gcube.dataanalysis.executor.rscripts.generic.GenericRScript

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

PARSED_AUTHORITY - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.RealTimeMatcher

PARSED_SCIENTIFIC_NAME - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.RealTimeMatcher

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

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.DistributedProcessingAgentWPS

PCAAInp - Static variable in class org.gcube.dataanalysis.executor.nodes.algorithms.ICCATVPA

PCAAInpURL - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.ICCATVPA

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

POST_PARSED_AUTHORITY - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.RealTimeMatcher

POST_PARSED_SCIENTIFIC_NAME - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.RealTimeMatcher

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.CMSY

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

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

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

PREPARSED_INPUT_DATA - Variable in class org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.RealTimeMatcher

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

printRConsole(Process) - Method in class org.gcube.dataanalysis.executor.util.LocalRScriptsManager

printRConsole(Process) - Static method in class org.gcube.dataanalysis.executor.util.RScriptsManager

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

process() - Method in class org.gcube.dataanalysis.executor.job.management.GenericWorker

process() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.WebApplicationPublisher

process() - Method in class org.gcube.dataanalysis.executor.rscripts.generic.GenericRScript

process() - Method in class org.gcube.dataanalysis.executor.rscripts.SGVMS_Interpolation

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

processOutput - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.ICCATVPA

processOutputParam - Static variable in class org.gcube.dataanalysis.executor.nodes.algorithms.ICCATVPA

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

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

PwaaInp - Static variable in class org.gcube.dataanalysis.executor.nodes.algorithms.ICCATVPA

PwaaInpURL - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.ICCATVPA

Q

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

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

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

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

read(Reader, char[], int, int) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Read characters from an input character stream.

read(Reader, char[]) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Read characters from an input character stream.

read(InputStream, byte[], int, int) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Read bytes from an input stream.

read(InputStream, byte[]) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Read bytes from an input stream.

readFileToByteArray(File) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Reads the contents of a file into a byte array.

readFileToString(File, Charset) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Reads the contents of a file into a String.

readFileToString(File, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Reads the contents of a file into a String.

readFileToString(File) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Reads the contents of a file into a String using the default encoding for the VM.

readFully(Reader, char[], int, int) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Read the requested number of characters or fail if there are not enough left.

readFully(Reader, char[]) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Read the requested number of characters or fail if there are not enough left.

readFully(InputStream, byte[], int, int) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Read the requested number of bytes or fail if there are not enough left.

readFully(InputStream, byte[]) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Read the requested number of bytes or fail if there are not enough left.

readLines(File, Charset) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Reads the contents of a file line by line to a List of Strings.

readLines(File, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Reads the contents of a file line by line to a List of Strings.

readLines(File) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Reads the contents of a file line by line to a List of Strings using the default encoding for the VM.

readLines(InputStream) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Get the contents of an InputStream as a list of Strings, one entry per line, using the default character encoding of the platform.

readLines(InputStream, Charset) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Get the contents of an InputStream as a list of Strings, one entry per line, using the specified character encoding.

readLines(InputStream, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Get the contents of an InputStream as a list of Strings, one entry per line, using the specified character encoding.

readLines(Reader) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Get the contents of a Reader as a list of Strings, one entry per line.

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

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

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

removeExtension(String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Removes the extension from a filename.

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

retrieveAddresses(String, String, String) - Static method in class org.gcube.dataanalysis.executor.util.InfraRetrieval

retrieveService(String, String) - Static method in class org.gcube.dataanalysis.executor.util.InfraRetrieval

retrieveServiceAddress(String, String, String, String) - Static method in class org.gcube.dataanalysis.executor.util.InfraRetrieval

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

RightSetStartIndexParameter - Static variable in class org.gcube.dataanalysis.executor.job.management.GenericWorker

RScriptsManager - Class in org.gcube.dataanalysis.executor.util

RScriptsManager() - Constructor for class org.gcube.dataanalysis.executor.util.RScriptsManager

run() - Method in class org.gcube.dataanalysis.executor.job.management.WPSJobManager.TasksWatcher

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

saveLogFile(String) - Method in class org.gcube.dataanalysis.executor.rscripts.generic.GenericRScript

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

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

scriptName - Static variable in class org.gcube.dataanalysis.executor.nodes.algorithms.ICCATVPA

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

sendNotification(String, String) - Method in class org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalInfraAlgorithm

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

separatorsToSystem(String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Converts all separators to the system separator.

separatorsToUnix(String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Converts all separators to the Unix separator of forward slash.

separatorsToWindows(String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Converts all separators to the Windows separator of backslash.

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

sessionID - Variable in class org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgentWPS

SessionParameter - Static variable in class org.gcube.dataanalysis.executor.job.management.GenericWorker

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

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

setCurrentOutputFileName(String) - Method in class org.gcube.dataanalysis.executor.util.LocalRScriptsManager

setCurrentOutputFileName(String) - Method in class org.gcube.dataanalysis.executor.util.RScriptsManager

setCurrentOutputURL(String) - Method in class org.gcube.dataanalysis.executor.util.LocalRScriptsManager

setCurrentOutputURL(String) - Method in class org.gcube.dataanalysis.executor.util.RScriptsManager

setInputParameters() - Method in class org.gcube.dataanalysis.executor.job.management.GenericWorker

setInputParameters() - Method in class org.gcube.dataanalysis.executor.nodes.transducers.WebApplicationPublisher

setInputParameters() - Method in class org.gcube.dataanalysis.executor.rscripts.generic.GenericRScript

setInputParameters() - Method in class org.gcube.dataanalysis.executor.rscripts.KnitrCompiler

setInputParameters() - Method in class org.gcube.dataanalysis.executor.rscripts.SGVMS_Interpolation

setInputParameters() - Method in class org.gcube.dataanalysis.executor.rscripts.TemplateRScripts

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

setStatus(float) - Method in class org.gcube.dataanalysis.executor.util.LocalRScriptsManager

setStatus(float) - Method in class org.gcube.dataanalysis.executor.util.RScriptsManager

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.CMSY

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

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

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

SGVMS_Interpolation - Class in org.gcube.dataanalysis.executor.rscripts

SGVMS_Interpolation() - Constructor for class org.gcube.dataanalysis.executor.rscripts.SGVMS_Interpolation

SGVMS_Interpolation.methodEnum - Enum in org.gcube.dataanalysis.executor.rscripts

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

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

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

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

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

shutdown() - Method in class org.gcube.dataanalysis.executor.rscripts.generic.GenericRScript

shutdown() - Method in class org.gcube.dataanalysis.executor.rscripts.SGVMS_Interpolation

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

sizeOf(File) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Returns the size of the specified file or directory.

sizeOfAsBigInteger(File) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Returns the size of the specified file or directory.

sizeOfDirectory(File) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Counts the size of a directory recursively (sum of the length of all files).

sizeOfDirectoryAsBigInteger(File) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Counts the size of a directory recursively (sum of the length of all files).

skip(InputStream, long) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Skip bytes from an input byte stream.

skip(Reader, long) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Skip characters from an input character stream.

skipFully(InputStream, long) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Skip the requested number of bytes or fail if there are not enough left.

skipFully(Reader, long) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Skip the requested number of characters or fail if there are not enough left.

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

StandardLocalInfraAlgorithm - Class in org.gcube.dataanalysis.ecoengine.interfaces

StandardLocalInfraAlgorithm() - Constructor for class org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalInfraAlgorithm

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

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

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

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

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

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

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

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

status - Variable in class org.gcube.dataanalysis.executor.util.LocalRScriptsManager

status - Variable in class org.gcube.dataanalysis.executor.util.RScriptsManager

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

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

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.CMSY

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

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

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

stop() - Method in class org.gcube.dataanalysis.executor.util.LocalRScriptsManager

stop() - Method in class org.gcube.dataanalysis.executor.util.RScriptsManager

StorageUtils - Class in org.gcube.dataanalysis.executor.util

StorageUtils() - Constructor for class org.gcube.dataanalysis.executor.util.StorageUtils

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

substituteStringInFile(String, String, String, String, boolean) - Static method in class org.gcube.dataanalysis.executor.util.LocalRScriptsManager

substituteStringInFile(String, String, String, String) - Static method in class org.gcube.dataanalysis.executor.util.RScriptsManager

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

TASK_FAILURE - Static variable in class org.gcube.dataanalysis.executor.job.management.GenericWorker

TASK_SUCCESS - Static variable in class org.gcube.dataanalysis.executor.job.management.GenericWorker

TASK_UNDEFINED - Static variable in class org.gcube.dataanalysis.executor.job.management.GenericWorker

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

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

TemplateRScripts - Class in org.gcube.dataanalysis.executor.rscripts

TemplateRScripts() - Constructor for class org.gcube.dataanalysis.executor.rscripts.TemplateRScripts

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

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

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

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

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

toBufferedInputStream(InputStream) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Fetches entire contents of an InputStream and represent same data as result InputStream.

toBufferedReader(Reader) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Returns the given reader if it is a BufferedReader, otherwise creates a toBufferedReader for the given reader.

toByteArray(InputStream) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Get the contents of an InputStream as a byte[].

toByteArray(InputStream, long) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Get contents of an InputStream as a byte[].

toByteArray(InputStream, int) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Get the contents of an InputStream as a byte[].

toByteArray(Reader) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Get the contents of a Reader as a byte[] using the default character encoding of the platform.

toByteArray(Reader, Charset) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Get the contents of a Reader as a byte[] using the specified character encoding.

toByteArray(Reader, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Get the contents of a Reader as a byte[] using the specified character encoding.

toByteArray(String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Deprecated.

Use String.getBytes()

toByteArray(URI) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Get the contents of a URI as a byte[].

toByteArray(URL) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Get the contents of a URL as a byte[].

toByteArray(URLConnection) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Get the contents of a URLConnection as a byte[].

toCharArray(InputStream) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Get the contents of an InputStream as a character array using the default character encoding of the platform.

toCharArray(InputStream, Charset) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Get the contents of an InputStream as a character array using the specified character encoding.

toCharArray(InputStream, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Get the contents of an InputStream as a character array using the specified character encoding.

toCharArray(Reader) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Get the contents of a Reader as a character array.

toFile(URL) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Convert from a URL to a File.

toFiles(URL[]) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Converts each of an array of URL to a File.

toInputStream(CharSequence) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Convert the specified CharSequence to an input stream, encoded as bytes using the default character encoding of the platform.

toInputStream(CharSequence, Charset) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Convert the specified CharSequence to an input stream, encoded as bytes using the specified character encoding.

toInputStream(CharSequence, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Convert the specified CharSequence to an input stream, encoded as bytes using the specified character encoding.

toInputStream(String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Convert the specified string to an input stream, encoded as bytes using the default character encoding of the platform.

toInputStream(String, Charset) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Convert the specified string to an input stream, encoded as bytes using the specified character encoding.

toInputStream(String, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Convert the specified string to an input stream, encoded as bytes using the specified character encoding.

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

toString(InputStream) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Get the contents of an InputStream as a String using the default character encoding of the platform.

toString(InputStream, Charset) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Get the contents of an InputStream as a String using the specified character encoding.

toString(InputStream, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Get the contents of an InputStream as a String using the specified character encoding.

toString(Reader) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Get the contents of a Reader as a String.

toString(URI) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Gets the contents at the given URI.

toString(URI, Charset) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Gets the contents at the given URI.

toString(URI, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Gets the contents at the given URI.

toString(URL) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Gets the contents at the given URL.

toString(URL, Charset) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Gets the contents at the given URL.

toString(URL, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Gets the contents at the given URL.

toString(byte[]) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Deprecated.

Use String.String(byte[])

toString(byte[], String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Get the contents of a byte[] as a String using the specified character encoding.

touch(File) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Implements the same behaviour as the "touch" utility on Unix.

toURLs(File[]) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Converts each of an array of File to a URL.

transferFileToService(String, String, String, int, String, String) - Static method in class org.gcube.dataanalysis.executor.util.DataTransferer

transferFileToService(String, String, String, int, String, String, String) - Static method in class org.gcube.dataanalysis.executor.util.DataTransferer

transferFileToService(String, String, String, int, String, String, String, boolean, String) - Static method in class org.gcube.dataanalysis.executor.util.DataTransferer

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

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

uploadFilesOnStorage(String, String, String, String, String, boolean) - Static method in class org.gcube.dataanalysis.executor.util.StorageUtils

uploadFilesOnStorage(String, String, String, String) - Static method in class org.gcube.dataanalysis.executor.util.StorageUtils

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

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.

valueOf(String) - Static method in enum org.gcube.dataanalysis.executor.rscripts.SGVMS_Interpolation.methodEnum

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.

values() - Static method in enum org.gcube.dataanalysis.executor.rscripts.SGVMS_Interpolation.methodEnum

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

W

waaInp - Static variable in class org.gcube.dataanalysis.executor.nodes.algorithms.ICCATVPA

waaInpURL - Variable in class org.gcube.dataanalysis.executor.nodes.algorithms.ICCATVPA

waitFor(File, int) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Waits for NFS to propagate a file creation, imposing a timeout.

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.WPSJobManager

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

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

wildcardMatch(String, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Checks a filename to see if it matches the specified wildcard matcher, always testing case-sensitive.

wildcardMatch(String, String, IOCase) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Checks a filename to see if it matches the specified wildcard matcher allowing control over case-sensitivity.

wildcardMatchOnSystem(String, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FilenameUtils

Checks a filename to see if it matches the specified wildcard matcher using the case rules of the system.

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

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

WPSJobManager.TasksWatcher - Class in org.gcube.dataanalysis.executor.job.management

write(File, CharSequence) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Writes a CharSequence to a file creating the file if it does not exist using the default encoding for the VM.

write(File, CharSequence, boolean) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Writes a CharSequence to a file creating the file if it does not exist using the default encoding for the VM.

write(File, CharSequence, Charset) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Writes a CharSequence to a file creating the file if it does not exist.

write(File, CharSequence, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Writes a CharSequence to a file creating the file if it does not exist.

write(File, CharSequence, Charset, boolean) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Writes a CharSequence to a file creating the file if it does not exist.

write(File, CharSequence, String, boolean) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Writes a CharSequence to a file creating the file if it does not exist.

write(byte[], OutputStream) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Writes bytes from a byte[] to an OutputStream.

write(byte[], Writer) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Writes bytes from a byte[] to chars on a Writer using the default character encoding of the platform.

write(byte[], Writer, Charset) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Writes bytes from a byte[] to chars on a Writer using the specified character encoding.

write(byte[], Writer, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Writes bytes from a byte[] to chars on a Writer using the specified character encoding.

write(char[], Writer) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Writes chars from a char[] to a Writer using the default character encoding of the platform.

write(char[], OutputStream) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Writes chars from a char[] to bytes on an OutputStream.

write(char[], OutputStream, Charset) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Writes chars from a char[] to bytes on an OutputStream using the specified character encoding.

write(char[], OutputStream, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Writes chars from a char[] to bytes on an OutputStream using the specified character encoding.

write(CharSequence, Writer) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Writes chars from a CharSequence to a Writer.

write(CharSequence, OutputStream) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Writes chars from a CharSequence to bytes on an OutputStream using the default character encoding of the platform.

write(CharSequence, OutputStream, Charset) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Writes chars from a CharSequence to bytes on an OutputStream using the specified character encoding.

write(CharSequence, OutputStream, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Writes chars from a CharSequence to bytes on an OutputStream using the specified character encoding.

write(String, Writer) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Writes chars from a String to a Writer.

write(String, OutputStream) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Writes chars from a String to bytes on an OutputStream using the default character encoding of the platform.

write(String, OutputStream, Charset) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Writes chars from a String to bytes on an OutputStream using the specified character encoding.

write(String, OutputStream, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Writes chars from a String to bytes on an OutputStream using the specified character encoding.

write(StringBuffer, Writer) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Deprecated.

replaced by write(CharSequence, Writer)

write(StringBuffer, OutputStream) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Deprecated.

replaced by write(CharSequence, OutputStream)

write(StringBuffer, OutputStream, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Deprecated.

replaced by write(CharSequence, OutputStream, String)

writeByteArrayToFile(File, byte[]) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Writes a byte array to a file creating the file if it does not exist.

writeByteArrayToFile(File, byte[], boolean) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Writes a byte array to a file creating the file if it does not exist.

writeLines(File, String, Collection<?>) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Writes the toString() value of each item in a collection to the specified File line by line.

writeLines(File, String, Collection<?>, boolean) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Writes the toString() value of each item in a collection to the specified File line by line, optionally appending.

writeLines(File, Collection<?>) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Writes the toString() value of each item in a collection to the specified File line by line.

writeLines(File, Collection<?>, boolean) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Writes the toString() value of each item in a collection to the specified File line by line.

writeLines(File, String, Collection<?>, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Writes the toString() value of each item in a collection to the specified File line by line.

writeLines(File, String, Collection<?>, String, boolean) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Writes the toString() value of each item in a collection to the specified File line by line.

writeLines(File, Collection<?>, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Writes the toString() value of each item in a collection to the specified File line by line.

writeLines(File, Collection<?>, String, boolean) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Writes the toString() value of each item in a collection to the specified File line by line.

writeLines(Collection<?>, String, OutputStream) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Writes the toString() value of each item in a collection to an OutputStream line by line, using the default character encoding of the platform and the specified line ending.

writeLines(Collection<?>, String, OutputStream, Charset) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Writes the toString() value of each item in a collection to an OutputStream line by line, using the specified character encoding and the specified line ending.

writeLines(Collection<?>, String, OutputStream, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Writes the toString() value of each item in a collection to an OutputStream line by line, using the specified character encoding and the specified line ending.

writeLines(Collection<?>, String, Writer) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.IOUtils

Writes the toString() value of each item in a collection to a Writer line by line, using the specified line ending.

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

writeStringToFile(File, String, Charset) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Writes a String to a file creating the file if it does not exist.

writeStringToFile(File, String, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Writes a String to a file creating the file if it does not exist.

writeStringToFile(File, String, Charset, boolean) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Writes a String to a file creating the file if it does not exist.

writeStringToFile(File, String, String, boolean) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Writes a String to a file creating the file if it does not exist.

writeStringToFile(File, String) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Writes a String to a file creating the file if it does not exist using the default encoding for the VM.

writeStringToFile(File, String, boolean) - Static method in class org.gcube.dataanalysis.executor.rscripts.generic.FileUtils

Writes a String to a file creating the file if it does not exist using the default encoding for the VM.

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

YearEndInp - Static variable in class org.gcube.dataanalysis.executor.nodes.algorithms.ICCATVPA

YearStartInp - Static variable in class org.gcube.dataanalysis.executor.nodes.algorithms.ICCATVPA

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