- GeneIdType - Class in peridot
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Lists the types of IDs available to be used on GeneOntology
- GeneIdType(String) - Constructor for class peridot.GeneIdType
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- get() - Static method in class peridot.Archiver.PeridotConfig
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- getAlreadyInstalled() - Method in class peridot.script.r.InstallationBatch
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- getAlternativeFileName(File) - Static method in class peridot.Archiver.Manager
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- getAnalysisParamsFromMap(Map<String, String>, Map<String, Class>) - Method in class peridot.CLI.AnalysisFileParser
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- getAvailableAnalysisModules() - Static method in class peridot.script.RModule
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- getAvailableInterpreters() - Static method in class peridot.script.r.Interpreter
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- getAvailableModules() - Static method in class peridot.script.RModule
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- getAvailableOrganisms() - Static method in class peridot.Organism
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Defines the default list of IDs available
- getAvailableParamTypes() - Static method in class peridot.AnalysisParameters
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- getAvailablePostAnalysisModules() - Static method in class peridot.script.RModule
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- getCommandArray(String) - Method in class peridot.script.r.Script
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- getCommands() - Method in class peridot.Output
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- getConditionOf(String) - Method in class peridot.AnalysisData
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- getConditionsFromExpressionFile(File, Spreadsheet.Info) - Static method in class peridot.AnalysisData
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- getConfigFile() - Method in class peridot.script.RModule
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- getConfigPath() - Method in class peridot.script.RModule
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- getConfigs() - Static method in class peridot.Archiver.PeridotConfig
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- getCurrentWorkingDir() - Static method in class peridot.Archiver.Manager
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- getDefaultColumnNames(int) - Static method in class peridot.Archiver.Spreadsheet
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- getDefaultHeader(int) - Static method in class peridot.Archiver.Spreadsheet
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- getDefaultIDTypes() - Static method in class peridot.GeneIdType
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Defines the default list of IDs available
- getDefaultModulesDir() - Static method in class peridot.Archiver.Places
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- getDefaultParameters() - Static method in class peridot.script.DiffExpressionModule
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- getDefaultParameters() - Static method in class peridot.script.PostAnalysisOntology
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- getDefaultRequiredFiles() - Static method in class peridot.script.DiffExpressionModule
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- getDefaultRequiredFiles() - Static method in class peridot.script.PostAnalysisOntology
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- getDefaultResults() - Static method in class peridot.script.DiffExpressionModule
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- getDefaultResults() - Static method in class peridot.script.PostAnalysisOntology
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- getDefaultRexecs() - Static method in class peridot.Archiver.Places
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- getDefaultValues() - Static method in class peridot.AnalysisParameters
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- getDescriptionFile() - Method in class peridot.script.RModule
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- getFailed() - Method in class peridot.script.r.InstallationBatch
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- getFirstCellPresent() - Method in class peridot.Archiver.Spreadsheet.Info
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- getFirstLinesFromFile(File, int) - Static method in class peridot.Global
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- getFirstRowFromFile(File, String) - Static method in class peridot.Archiver.Spreadsheet
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- getFromQueue() - Method in class peridot.Output
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- getHeaderOnFirstLine() - Method in class peridot.Archiver.Spreadsheet.Info
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- getInfo() - Method in class peridot.Archiver.Spreadsheet
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- getInputFiles() - Method in class peridot.script.RModule
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- getInterpreterNumber() - Static method in class peridot.CLI.PeridotCmd
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- getInterpretersStr() - Static method in class peridot.script.r.Interpreter
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- getJarFolder() - Static method in class peridot.Archiver.Places
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- getLabelsOnFirstCol() - Method in class peridot.Archiver.Spreadsheet.Info
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- getLinuxEnvVars() - Method in class peridot.script.r.Interpreter
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- getLogger() - Static method in class peridot.Log
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- getMandatoryResults() - Static method in class peridot.script.DiffExpressionModule
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- getName() - Method in class peridot.script.ScriptExec
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- getNamesAndConditions() - Method in class peridot.AnalysisData
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- getNaturallyWritenString(String) - Static method in class peridot.Global
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Changes a String from programming notation to a more "natural" form.
- getNoPermission() - Method in class peridot.script.r.InstallationBatch
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- getNotExistantResults() - Method in class peridot.script.RModule
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- getNumber() - Method in class peridot.IndexedString
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- getNumberOfConditions() - Method in class peridot.AnalysisData
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- getNumberOfGenes() - Method in class peridot.AnalysisData
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- getNumberOfSamples() - Method in class peridot.AnalysisData
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- getOutputStr() - Method in class peridot.script.r.PackageInstaller
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- getOutputStream() - Method in class peridot.script.r.Script
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- getOutputString() - Method in class peridot.script.r.Script
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- getPackage() - Method in class peridot.script.r.PackageInstaller
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- getPackageListStr(Collection<Package>) - Static method in class peridot.CLI.PeridotCmd
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- getPackageName() - Method in class peridot.script.r.PackageInstaller
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- getPackagesToInstall() - Method in class peridot.script.r.Interpreter
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- getParamsDescription() - Method in class peridot.script.RModule
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- getRequiredParametersFromModules() - Static method in class peridot.script.RModule
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- getRequiredParamsFromModules() - Method in class peridot.CLI.AnalysisFileParser
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- getRequiredScripts() - Static method in class peridot.script.PostAnalysisOntology
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- getRows() - Method in class peridot.Archiver.Spreadsheet
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- getRows(int) - Method in class peridot.Archiver.Spreadsheet
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- getRowsFromTable(File, int, String) - Static method in class peridot.Archiver.Spreadsheet
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- getRunningTask() - Static method in class peridot.script.Task
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- getRVersion() - Method in class peridot.script.r.Interpreter
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- getScriptFile() - Method in class peridot.script.RModule
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- getScriptPath() - Method in class peridot.script.RModule
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- getScriptType() - Method in class peridot.script.RModule
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- getSeparator() - Method in class peridot.Archiver.Spreadsheet
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- getSpecification() - Static method in class peridot.CLI.AnalysisFile
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- getSpecificParams() - Method in class peridot.CLI.AnalysisFileParser
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- getSubDirs(File) - Static method in class peridot.Archiver.Manager
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Retrieves the subdirectories of a directory
- getSuccessful() - Method in class peridot.script.r.InstallationBatch
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- getText() - Method in class peridot.IndexedString
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- getText() - Method in class peridot.Output
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- getUserHomePath() - Static method in class peridot.Archiver.Places
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- getWin64And32ExecsFrom(String) - Static method in class peridot.Archiver.Places
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- getWorkingDirectory() - Method in class peridot.script.RModule
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- getWorkingDirectoryPath() - Method in class peridot.script.RModule
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- Global - Class in peridot
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Global general purpose functions.
- Global() - Constructor for class peridot.Global
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- Global.RoundingMode - Enum in peridot
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- guessLineSeparator(File) - Static method in class peridot.Archiver.Spreadsheet.Info
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