- abort() - Method in class peridot.script.ScriptExec
-
- abortAll() - Method in class peridot.script.Task
-
- abortAllFlag - Variable in class peridot.script.Task
-
- addFinished(String, boolean) - Method in class peridot.script.Task
-
- addInterpreter(String) - Static method in class peridot.CLI.PeridotCmd
-
- addInterpreter(String) - Static method in class peridot.script.r.Interpreter
-
- addToQueue(PackageInstaller) - Method in class peridot.script.r.InstallationBatch
-
- afterEnd() - Method in class peridot.script.r.Script
-
- afterStart(boolean) - Method in class peridot.script.r.Script
-
- afterStart() - Method in class peridot.script.ScriptExec
-
- allInfo - Variable in class peridot.CLI.AnalysisFile
-
- allInfo - Variable in class peridot.CLI.AnalysisFileParser
-
- allInfoSet() - Method in class peridot.Archiver.Spreadsheet.Info
-
- analyseInterpreter() - Method in class peridot.script.r.Interpreter
-
- AnalysisData - Class in peridot
-
Manages the count reads file and all the meta-information about it.
- AnalysisData(File, File, Spreadsheet.Info, String, int) - Constructor for class peridot.AnalysisData
-
- AnalysisData(File, SortedMap<IndexedString, String>, Spreadsheet.Info, String, int) - Constructor for class peridot.AnalysisData
-
- AnalysisFile - Class in peridot.CLI
-
A file with all the definitions necessary to do an analysis.
- AnalysisFile(File) - Constructor for class peridot.CLI.AnalysisFile
-
- AnalysisFile() - Constructor for class peridot.CLI.AnalysisFile
-
- analysisFile - Variable in class peridot.CLI.AnalysisFileParser
-
- AnalysisFileParser - Class in peridot.CLI
-
Parses an AnalysisFile file to the AnalysisFile object.
- AnalysisFileParser(File) - Constructor for class peridot.CLI.AnalysisFileParser
-
- AnalysisFileParser.ParseException - Exception in peridot.CLI
-
- AnalysisModule - Class in peridot.script
-
- AnalysisModule(String, String, Map<String, Class>, Set<String>, Set<String>) - Constructor for class peridot.script.AnalysisModule
-
- AnalysisModule(File) - Constructor for class peridot.script.AnalysisModule
-
- AnalysisParameters - Class in peridot
-
The parameters necessary for an analysis.
- AnalysisParameters() - Constructor for class peridot.AnalysisParameters
-
Creates an empty AnalysisParameters
- AnalysisParameters(Map<String, Class>) - Constructor for class peridot.AnalysisParameters
-
Creates AnalysisParameters defining the required parameters.
- AnalysisParameters(Map<String, Class>, Map<String, Object>) - Constructor for class peridot.AnalysisParameters
-
Creates a ready AnalysisParameters, with both definition of
required parameters and parameters.
- appendChar(char) - Method in class peridot.Output
-
- appendLine(String) - Method in class peridot.Output
-
- applyConditionsToExprFileSamples(File, Spreadsheet.Info, SortedMap<IndexedString, String>) - Static method in class peridot.AnalysisData
-
- args - Variable in class peridot.CLI.Command
-
- askToUpdateInterpreter(int) - Static method in class peridot.CLI.PeridotCmd
-
- availableInterpreters - Variable in class peridot.Archiver.PeridotConfig
-
- availableModules - Static variable in class peridot.script.RModule
-
- availablePackages - Variable in class peridot.script.r.Interpreter
-
- availableParamTypes - Static variable in class peridot.AnalysisParameters
-
- availableParamTypes - Static variable in class peridot.script.RModule
-