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D

dataStr - Static variable in class peridot.CLI.AnalysisFileParser
 
defaultBuilderOperations(File, File, Spreadsheet.Info, String, int) - Method in class peridot.AnalysisData
 
defaultDBs - Static variable in class peridot.Organism
The list of default ID types.
defaultIDTypes - Static variable in class peridot.GeneIdType
The list of default ID types.
defaultInterpreter - Variable in class peridot.Archiver.PeridotConfig
 
defaultInterpreter - Static variable in class peridot.script.r.Interpreter
 
defaultModulesDir - Static variable in class peridot.Archiver.Places
The directory where the defaults module, that can be loaded to modulesDir, are stored.
defaultRportableDirs() - Static method in class peridot.Archiver.Places
 
defineAvailableParamTypes() - Static method in class peridot.script.RModule
 
defineCmdNameAndDetails() - Method in class peridot.CLI.Command
 
defineCmdNameAndDetails() - Method in class peridot.CLI.Commands.IN
 
defineCmdNameAndDetails() - Method in class peridot.CLI.Commands.LS
 
defineCmdNameAndDetails() - Method in class peridot.CLI.Commands.OUT
 
defineCmdNameAndDetails() - Method in class peridot.CLI.Commands.R
 
defineCmdNameAndDetails() - Method in class peridot.CLI.Commands.RUN
 
defineCommand(Interpreter) - Method in class peridot.script.r.Script
 
defineCommand() - Method in class peridot.script.ScriptRunnable
 
defineIsRunningRunnable() - Method in class peridot.script.ScriptExec
 
defineStatusWatcher() - Method in class peridot.script.Task
 
defineZombieFinder() - Method in class peridot.script.Task
 
deletePeridotFolder() - Static method in class peridot.Global
Delete the whole r-peridot-files folder.
deleteScript(String) - Static method in class peridot.script.RModule
 
detail - Variable in class peridot.CLI.Command
 
detectPreviousRunn() - Method in class peridot.script.ScriptRunnable
 
DiffExpressionModule - Class in peridot.script
 
DiffExpressionModule(String, String, boolean, boolean) - Constructor for class peridot.script.DiffExpressionModule
 
DiffExpressionModule(File) - Constructor for class peridot.script.DiffExpressionModule
 
dirExists(String) - Static method in class peridot.Archiver.Manager
Checks for the existence of a directory.
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